Final Report Summary - CIBIO-NEW-GEN (Capacity building at CIBIO for research using Next-Gen Sequencing)
Executive Summary:
The work of CIBIO-New-Gen project was divided into 8 different Work Packages. A summary of the achievements regarding those Work Packages for the entire project period is outlined below:
Acquisition and implementation of a Next Generation Sequencing platform and recruitment of experienced researchers
Implementation of the high and medium throughput/output platform unit at CIBIO
A high and medium throughput/output sequencing platform was implemented at the CIBIO facilities. The selected Illumina HiSeq 1500 and the Illumina benchtop MiSeq sequencers were installed in September 2013. The acquisition also included a variety of support equipment to make the NGS workflow complete and fully functional. Following the implementation of the platform, a period of in-house test runs and protocol implementations were performed. CIBIO is currently able to provide a number specific NGS and downstream data analyses services both internally at the institute as well as nationally in Portugal (see NewGen website for service information – http://cibio-newgen.pt/).
Recruitment of experienced researchers
The employment of two experienced researchers with extensive experience in the area of sequencing by synthesis as well as data analysis was fulfilled. After a thorough recruitment process the first selected candidate was Dr. Nadia de Moraes Barros. Dr. Barros holds a PhD in Genetics and Evolutionary Biology (Biosciences Institute, University of S. Paulo, Brazil). The second selected candidate was Dr. Filipe Jorge Garret Vieira. Dr. Vieira has a PhD in Biological Sciences (University of Barcelona, Spain), as well as Post-Doc experience at UC Berkeley, USA, with a special emphasis on Next-Generation Sequencing (NGS) data.
Improvement of data analysis capacity at CIBIO & initiation and implementation of a bioinformatics group
Acquisition of a “Genomics Factory”: computer capacity and software
A data storage and a linked powerful computing cluster was acquired and implemented. The choice fell an a Isilon X400 (x3) data storage unit with the capacity of up 108 TB, and a computing/server cluster consisting of 5 nodes (one computer with 1 TB RAM, 4 processors, 8C and four computers with 256 GB RAM, 4 processors, 8C. One node of the four smaller computers was installed at the CIBIO site in Vairão, and the Isilon storage unit and the rest of the computing cluster was installed at one of University of Porto´s (UP) data centers. The overall acquisition process and the implementation was guided and advised by Dr. Nuno Fonseca (EBI, Cambridge, UK), Dr. Filipe Vieira, who was hired as a research scientist for the CIBIO-New-Gen project, and who decided to accept a job offer at the Natural History Museum of Denmark, and the two bioinformaticians (see below) hired towards the end of 2014. CIBIO is currently able to provide a number of NGS application services as well as complex data analysis support.
Recruitment of two Bioinformaticians and three Research Scientist
Recruitment of two bioinformaticians with expertise in Bioinformatics, Computational biology and Next Generation Sequencing data analysis
Following a thorough selection procedure the two positions were filled with the following researchers:
Dr. Antonio Muñoz - Dr. Munñoz holds a PhD in Computational Biology and Bioinformatics. He brings along a solid expertise in data analysis as well as software development from a large variety of different projects ranging from fruit quality determination, olive transcriptome assembly and annotation, as well as hospital connected biomedical projects, and Dr. John Archer - Dr. Archer holds a PhD in computational biology from the University of Manchester, UK and brings along expertise in analysis of NGS data, statistics, algorithm development, software development, recombination analysis, sequence alignment and phylogeny. During his PhD he developed and implemented the first NGS read mapper capable of mapping reads derived from highly variable data sources such as rapidly evolving RNA viral populations.
High-skilled research scientist recruitment
Three Post-Doc fellows were recruited (see below), all were very well integrated at CIBIO and developed their work as expected. However, we had to re-recruit/replace the holder of Position 1 two times since the contract holders decided to explore other carrier opportunities during the contract period.
Selected candidates:
Position 1. Dr. Wen-Ya Ko - Dr. Ko holds a PhD in Biology (Molecular Evolutionary Biology option), Pennsylvania State University, USA. He has a very solid expertise regarding both experimental and theoretical approaches including DNA and phenotypic/clinical data collection in the field, molecular biology experiments in laboratory, computational programming for data analysis, and development of statistical tools for identifying signatures of evolutionary adaptation in the human genome.
Position 1 - replacement/re-recruitment (for Dr. Ko)
Dr. Daniel Vasco - Dr Vasco holds a PhD in Mathematical Biology from the University of Texas, and he brought along extensive expertise in the areas of Programming, Bioinformatics data analysis (Large-scale (massive) next generation data analysis and critical assessment, relational data bases (my SQL), SNP and microarray data, genomic signal analysis), Applied mathematics, computational modeling and statistics (stochastic simulation, algorithm testing and evaluation, algorithm development and implementation on multiple platforms), as well as Matched experimental and computational protocols for single-cell genomics and transcriptomics.
Position 1 - replacement/re-recruitment (for Dr. Vasco)
Dr. Magda Gaya - Dr. Gaya holds a PhD in Human Population Genetics from the University of Barcelona and brings along extensive expertise in comparative and functional genomics related to Human polymorphic inversions and Molecular evolution, Biomedical Bioinformatics – Adaptive evolution in the human lineage, and functional analysis of genomes, among other skills.
Position 2. Dr. Ana Assunção - Dr. Assunção holds a PhD in Ecology and Ecotoxicology of Plants from the Free University of Amsterdam, The Netherlands. She has worked as researcher and project coordinator (NWO-VENI laureate) at the Laboratory of Genetics at Wageningen University, the Netherlands, and at the Department of Plant Biology and Biotechnology at University of Copenhagen, Denmark.
Position 3. Dr. Natália Dias - Dr. Dias holds a PhD in Marine Ecology from the University of Algarve, and has solid research experience in ecology, biology and evolutionary ecology from a top Environmental Sciences School (School of Environmental Sciences, University of East Anglia, UK) and the University of Valencia. She brought along solid expertise in coordination of large-scale international collaboration in research and post-graduation education involving a top world university (MIT) and all the main Portuguese universities
Twinning: Expertise and know-how exchange, and Training for knowledge transfer to CIBIO
In total almost thirty training and exchange activities (WP5) and eleven know-how transfer and mobility activities (WP6) have been executed during the project period, involving PI´s, other experienced staff as well as junior or early stage career researchers. The visits have focused mainly on Next Generation Sequencing techniques implementation, protocol set-up as well as the downstream sequence data analyses methodologies. The exchange and twinning activities also served for an improved integration of CIBIO in the European Research Area, through long lasting partnerships with research groups in Europe, as well as with American partner institutions, and several important research areas in the context of Next Generation Sequencing have been/are being addressed.
Workshops, conferences, dissemination and visibility
Updating CIBIO´s website/Implementation of the dedicated CIBIO New-Gen project website
A new CIBIO’s website as well as a CIBIO-New-Gen project dedicated website were implemented and the websites have been continuously updated regarding project activities/news as well as new sequencing services being provided throughout the project.
Conference participation and Organization of international workshops, national meetings and courses
Seventeen participations by CIBIO researchers at 10 different high-level international conferences have taken place and numerous international workshops, national meetings and courses have been organized during the course of the CIBIO-New-Gen project as outlined in the report and deliverables. These activities have had a huge impact regarding the opportunities for researchers from a large number of research groups at CIBIO to disseminate and discuss their scientific results and findings at these different venues and events.
TV documentaries
A production of a series of TV-documentaries on biodiversity has been concluded and resulted in a unique project of science dissemination. The series of documentaries will be broadcasted in the Portuguese first TV channel RTP1 on prime time.
Publication of booklets
Two booklets disseminating the information about the current Next Generation Sequencing project activities at CIBIO have been produced. The booklets cover NGS approaches in the fields of Conservation, Metagenomics and Evolution.
Organization of Seminars including FP7 encouragement topic and establishment of consortia
6 seminars have been organized within the context of the CIBIO-New-Gen project under the course of the project. These seminars were disseminated widely and were open for researchers from other scientific institutes, companies with interest in the scientific field as well as the general public.
In the context of the impact and benefits of the NewGen project here, CIBIO has become a partner of a recently approved FCT (National Foundation for Science and Technology) Research Infrastructure, GenomePortugal, as well as the leading/coordinating Institution for a second approved FCT Research Infrastructure, PORBIOTA.
Society/Industry/SMEs info days and impact
A number of combined scientific and Next Generation Sequencing platform information days, open to researchers, companies and the public in general, have been organized. The impact of the mentioned meetings (as well as the additionally organized meetings and seminars) was great. We have had a number of service requests/collaboration proposals from other research institutes, governmental organizations (e.g. the Portuguese National Institute for Health), and a number of hospitals. Some of these activities are already ongoing and others are currently being planned.
In addition, we continue our collaboration with StabVida regarding commercialization of services related to genetics and are in negotiations regarding collaborations on Next Generation Sequencing service provision.
CIBIO is also in conclusive negotiations with representatives from a French biotech company (ANTAGENE), regarding establishing a spin-off company at the CIBIO campus in Vairão (collaboration regarding NGS services and applications).
CIBIO has furthermore ongoing collaboration protocols and support with/from EDP – “Energias de Portugal, S.A.” in the area of biodiversity and is also coordinating a REN Chair in Biodiversity (co-sponsored by REN – National Energy Networks and FCT - the Portuguese national funding agency for science, research and technology).
Project Context and Objectives:
The focus of research at CIBIO is evolutionary biology, conservation genetics, and ecology in a conservation context. A large part of research lines employs the DNA level analysis of biological diversity. During the last years, new technologies arose in this field, which provide today the opportunity to generate new types of datasets with especially high information content for genome based investigation of biological diversity. The CIBIO- New-Gen proposal has two main objectives: 1) to install New Generation sequencing platforms and integrate the respective techniques in CIBIO scientists research, and 2) to equip the unit with the computer infrastructure necessary to handle the increasing amount of data and analytical procedures for downstream sequence analysis and for modeling approaches. This activity will be accompanied by strengthening our research staff and by training and exchange of expertise in collaboration with international partners. The acquisition and implementation of the new technologies and the development of the respective expertise will enable the institution to fully develop its potential in quality of research and international recognition.
As indicated above the CIBIO unit intents through this REGPOT project to strengthen its impact on a regional and international scale by using an integrated approach that involves the acquisition of research equipment to remain internationally competitive, the acquisition of additional expertise to implement this equipment, the intensification of dissemination activities to foster its international recognition and to further reinforce its involvement in regional and national stakeholder activities.
Moreover, an overall objective is also to ensure that CIBIO becomes a full participant of the European Research Area (ERA), reinforces its excellence and creativity and be able to take advantage of the knowledge and know-how existing in high ranking institutions in Europe (e.g. the MPI for evolutionary anthropology and Uppsala University) and the USA (e.g. University of California, Berkeley), all of them world leading research organizations. With the implementation of this project, CIBIO’s active contribution to the regional economy and social welfare will be significantly increased.
Project Results:
Project objectives and description of main S & T results
Description of the overall Project objectives
The focus of research at CIBIO is evolutionary biology, conservation genetics, and ecology in a conservation context. A large part of research lines employs the DNA level analysis of biological diversity. During the last years, new technologies arose in this field, which provide today the opportunity to generate new types of datasets with especially high information content for genome based investigation of biological diversity. The CIBIO-New-Gen project had two main objectives: 1) to install New Generation sequencing platforms and integrate the respective techniques in CIBIO’s research, and 2) to equip the unit with the computer infrastructure necessary to handle the increasing amount of data and analytical procedures for downstream sequence analysis and for modeling approaches. These activities were accompanied by strengthening our research and by training staff and exchanging expertise in collaboration with international partners. The acquisition and implementation of the new technologies and the development of the respective expertise enabled the institution to develop its potential research quality and international recognition.
CIBIO intended, through this REGPOT project, to strengthen its impact at a regional and international scales by using an integrated approach involving the acquisition of research equipment to remain internationally competitive, the acquisition of additional expertise to implement this equipment, the intensification of dissemination activities to foster its international recognition and to further reinforce its involvement with regional and national stakeholders.
Moreover, an overall objective was also to ensure that CIBIO becomes a significant participant in the European Research Area (ERA), reinforcing its excellence and creativity and being able to take advantage of the knowledge and know-how existing in world leading research institutions in Europe (e.g. the MPI for evolutionary anthropology and Uppsala University) and US (e.g. University of California, Berkeley).
The results of the CIBIO-New-Gen project allowed CIBIO to strengthen significantly its research profile and potential, raising its capacity to establish collaborations both at national and international levels. The acquisition of the most powerful next generation genome sequencer in Portugal and the extensive interchange program for students and researchers allowed the institute to upgrade its research and computing infrastructure and to train its staff in new cutting edge methodologies used in the emerging area of genomics. All of this turned the institute much more attractive for researchers and research institutions. This capacity is most relevant not only for attracting new talent and collaborations but also for retaining talent, reversing brain drain, and developing into higher levels existing collaborations. Through the CIBIO-New-Gen project, CIBIO became a stronger player both in the Portuguese research system and in the European Research Area.
The work of CIBIO-New-Gen project was divided into 8 different Work Packages. The achievements regarding those Work Packages for the entire project period are reported below:
Acquisition and implementation of a Next Generation Sequencing platform and recruitment of experienced researchers
Implementation of the high and medium throughput/output platform unit at CIBIO
According to the objectives of WP1 and 2, a high and medium throughput/output sequencing platform were implemented at CIBIO facilities. The selected Illumina HiSeq 1500 (plus the cBot device) and the Illumina benchtop MiSeq sequencers were installed in September 2013. This reversible-terminator sequencing by synthesis technology (TruSeq chemistry) based system features two run modes, rapid run and high output run mode, providing a flexible and scalable platform that supports a broad range of applications and study sizes such as Targeted resequencing, gene expression, whole-genome sequencing and epigenetics. As indicated, HiSeq 1500 system also features the cBot, a stand-alone automated system that creates clonal clusters from single molecule DNA templates. The acquisition also included a variety of support equipment to make the Next Generation Sequencing workflow complete and fully functional.
Following the implementation of the platform, a period of in-house test runs and protocol implementations were performed with the aim of setting up the Next Generation Sequencing (NGS) services properly. CIBIO is currently able to provide a number specific NGS and downstream data analyses services both internally at the institute as well as nationally in Portugal. A number of recently concluded, as well as still ongoing sequencing, projects have been performed/are being executed, involving a wide range of taxonomic groups of organisms such as mammals, birds, reptiles, fish, several invertebrates and plants: Brindle rabbit, Plumage color canary, Singing varieties canary, Palanca (giant sable antelope), Littorina (sea snails), Hares, Human, Alosa (shad), Scorpions, Deer, and Wine (see NewGen website for service information – http://cibio-newgen.pt/). The Next Generation sequencing services currently implemented and provided are: Whole genome sequencing, RNA-seq, RAD sequencing, Transcriptome sequencing and Metagenomics sequencing
Recruitment of experienced researchers
The employment of two experienced researchers with extensive experience in the area of sequencing by synthesis as well as data analysis was fulfilled. After a thorough recruitment process the first selected candidate was Dr. Nadia de Moraes Barros. Dr. Barros holds a PhD in Genetics and Evolutionary Biology (Biosciences Institute, University of S. Paulo, Brazil). She worked as a postdoctoral researcher at the Laboratory of Evolutionary Biology and Vertebrate Conservation (Labec, IB-USP, Brazil). Her research focus is on conservation genetics in Neotropics and she brings along experience in phylogeography, phylogeny, comparative morphological analyses, population genetics and the use of Next Generation Sequencing in selecting molecular markers for endangered and non-model species.
The second selected candidate was Dr. Filipe Jorge Garret Vieira. Dr. Vieira has a PhD in Biological Sciences (University of Barcelona, Spain), as well as Post-Doc experience at UC Berkeley, USA, with a special emphasis on Next-Generation Sequencing (NGS) data. Here he was focusing on two main topics: i) the development of Next Generation Sequencing methods for the analysis of low coverage/quality data; and ii) the study of rice domestication to better understand its origin and dissemination.
Dr. Barros is still contracted at CIBIO and Dr. Vieira has moved to a new position at the University of Copenhagen.
Impact as a result of the CIBIO-New-Gen project (applying to the 2 above described Work packages)
As a direct impact of the CIBIO-New-Gen funding CIBIO was able to seek and get approval of substantial additional funding in the context of capacity building through Next Generation Sequencing. Examples of additional achieved funding are:
1) GenomePortugal (National Facility for Genome Sequencing and Analysis; CIBIO is a member of this FCT funded Research Infrastructure). GenomePortugal is a distributed genome sequencing and analysis RI for basic/applied genome research and advanced services, and the network covers all research centers and governmental institutes with NGS equipment in Portugal.
2) CIBIO – Genomics, Biodiversity and Evolution – funding from the ON2 Programme, by the Regional Governmental body CCDR-n, from Structural funds - consumables and additional small laboratory equipment related to major sequencing projects currently performed at CIBIO (for example the full and de novo sequencing of the Giant Sable Antelope genome from Angola, an animal in the brink of extinction, and with global visibility, which is the national symbol of Angola).
3) Additional funds for a series of research contracts and post-doctoral positions were granted by the National Foundation for Science and Technology (FCT). These successful proposals, strongly benefitted from this project as they will be all using the new NGS and bioinformatics platform.
Improvement of data analysis capacity at CIBIO & initiation and implementation of a bioinformatics group
The objectives were to recruit a Head for a new Bioinformatics Core group followed by the installation of the “Genomics Factory” supervised by the new Head. As described in the mid-term report, these Tasks could not been performed as planned and within the first set timelines, but a solution/deviation for making progress regarding this crucial work package was achieved during the final reporting period (see below).
Acquisition of a “Genomics Factory”: computer capacity and software
We were not able to hire a person for the position of Head of the Core Bioinformatics group under this work package, but an agreement was made with the selected top candidate for the position, Dr. Fonseca (EBI, Cambridge, UK) to work as an advisor in the process of the Genomics Factory acquisition and implementation. Similarly, Dr. Garett Vieira, who was hired as a research scientist (with specific NGS bioinformatics expertise, see above), and who decided to accept a job offer at the Natural History Museum of Denmark (University of Copenhagen), also agreed to continue to provide expert advice after his move to Denmark. The two bioinformaticians hired towards the end of 2014 were also heavily involved in the implementation process of the overall Genomics Factory, in particular regarding the final installations of the data storage unit and the computing server clusters. Regarding the purchase process of the Data Storage and the linked computing cluster, an official tender process was performed and following a thorough selection process with an important involvement by the team of advisors/consultants mentioned above, the choice fell on purchasing an Isilon X400 (x3) data storage unit with the capacity of up 108 TB, and a computing/server cluster consisting of 5 nodes (one computer with 1 TB RAM, 4 processors, 8C and four computers with 256 GB RAM, 4 processors, 8C. One node of the four smaller computers was installed at the CIBIO site in Vairão, and the Isilon storage unit and the rest of the computing cluster was installed at one of University of Porto´s (UP) data centers (at the Faculty of Sciences). The latter installation is giving us access to UPs experienced technical/maintenance team as well as direct connection/access to additional storage capacity and computing clusters already existing at this site. The overall NGS and bioinformatics platform is up and running and we have already performed a number of sequencing projects and downstream bioinformatics data analyses. We have, in addition, organized several courses/workshops making use of the installed data analysis equipment and software.
Impact as a result of the CIBIO-New-Gen project overall and specifically the improvement of the bioinformatics capacities at CIBIO
As a result of the CIBIO-New-Gen project and here specifically the installation and implementation of the powerful data computing and storage equipment, CIBIO was able to earn a series of extremely important additional funds which put our research centre in a very competitive position both nationally and in the European Research Area (ERA).
CIBIO is the leader institute and the CIBIO-New-Gen Coordinator is the PI for a National Consortium/Research Infrastructure (RI), PORBIOTA (the Portuguese E-Infrastructure for Information and Research on Biodiversity), which is in the future expected to become the Portuguese node of the European ESFRI LifeWatch. This Research Infrastructure is funded by the Portuguese Foundation for Science and Technology and the funding covers additional computing and storage power, as well as resources for hiring researchers and technicians to work within the data analyses workflow resulting from massive sequencing projects using our Genomics Platform facility.
In addition we were also able to recruit two skilful bioinformaticians, forming the primary structure of a well-needed bioinformatics group at CIBIO (more details below under recruitment). Our intension is to expand this group, by hiring bioinformatics technicians and researchers, e.g. via the above indicated PORBIOTA research infrastructure funding.
Recruitment of two Bioinformaticians and three Research Scientist
Background
As indicated in the mid-term report, the recruitment objectives for this work package had at that time been fulfilled except for the recruitment of the Principal Investigator for Computational and Theoretical Biology. For this position, and in the context of the difficulties in employing senior researchers in the areas of bioinformatics and computational biology, it was agreed with the EC (the project officer) to split this position into two positions for slightly less senior bioinformatics, computational biology and NGS data analysis positions.
Specific advertisements for the experienced research and bioinformatics positions (see below) were published in scientific journals of high circulation and visibility, mobility networks like EraCareers, Euraxess, and Marie Curie Fellowships association, social networks as well as via e-mailing to international research partners and collaborators.
Recruitment of two bioinformaticians with expertise in Bioinformatics, Computational biology and Next Generation Sequencing data analysis
Following a thorough selection procedure the two positions were filled with the following researchers:
Dr. Antonio Muñoz - Dr. Munñoz holds a PhD in Computational Biology and Bioinformatics. He brings along a solid expertise in data analysis as well as software development from a large variety of different projects ranging from fruit quality determination, olive transcriptome assembly and annotation, as well as hospital connected biomedical projects. For further details on Dr. Muñoz background as well the NewGen project activities he has been involved in, please see his NewGen activity report link in the final periodic report.
and
Dr. John Archer - Dr. Archer holds a PhD in computational biology from the University of Manchester, UK and brings along expertise in analysis of NGS data, statistics, algorithm development, software development, recombination analysis, sequence alignment and phylogeny. During his PhD he developed and implemented the first NGS read mapper capable of mapping reads derived from highly variable data sources such as rapidly evolving RNA viral populations. His postdoctoral research was driven by national and international collaborations, involving investigations regarding the emergence of drug resistance mutations within HIV-1 populations as well as the development of a viral genotyping tool. He has furthermore developed an assembly tool capable of assembling of non- chimeric contigs from read datasets harbouring isoform variation, being the first such tool that successfully archives this task. For further details on Dr. Archers background as well the NewGen project activities he has been involved in please, see his NewGen activity report link in the final periodic report.
High-skilled research scientist recruitment
Three Post-Doc fellows were recruited (see below), all were very well integrated at CIBIO and developed their work as expected. However, we had to re-recruit/replace the holder of Position 1 two times since the contract holders decided to explore other carrier opportunities during the contract period.
Selected candidates:
Position 1. Dr. Wen-Ya Ko - Dr. Ko holds a PhD in Biology (Molecular Evolutionary Biology option), Pennsylvania State University, USA. He has a very solid expertise regarding both experimental and theoretical approaches including DNA and phenotypic/clinical data collection in the field, molecular biology experiments in laboratory, computational programming for data analysis, and development of statistical tools for identifying signatures of evolutionary adaptation in the human genome. Dr. Ko decided to leave CIBIO because he had an offer of a tenure track faculty position in his home country (Taiwan). Please see the activity report during his contract period (link in final periodic report).
Position 1 - replacement/re-recruitment
Following a careful selection procedure to substitute Dr. Wen-Ya Ko, a decision was made to hire Dr. Daniel Vasco. Dr Vasco holds a PhD in Mathematical Biology from the University of Texas, and he brought along extensive expertise in the areas of Programming, Bioinformatics data analysis (Large-scale (massive) next generation data analysis and critical assessment, relational data bases (my SQL), SNP and microarray data, genomic signal analysis), Applied mathematics, computational modeling and statistics (stochastic simulation, algorithm testing and evaluation, algorithm development and implementation on multiple platforms), as well as Matched experimental and computational protocols for single-cell genomics and transcriptomics.
During the contract period Dr. Vasco made the decision to pursue other carrier opportunities and to leave this position. Please see the activity report during his contract period (link in final periodic report).
Position 1 - replacement/re-recruitment (2nd). Dr. Magda Gaya
After an additional thorough selection procedure to substitute Dr. Vasco, a decision was made to recruit Dr. Magda Gaya. Dr. Gaya holds a PhD in Human Population Genetics from the University of Barcelona and brings along extensive expertise in comparative and functional genomics related to Human polymorphic inversions and Molecular evolution, Biomedical Bioinformatics – Adaptive evolution in the human lineage, and functional analysis of genomes, among other skills.
For details regarding Dr. Gaya’s NewGen project activities during her contract period, please see the final periodic report.
Position 2. A research scientist was hired for the position related to studies on plant adaptation to abiotic stress, in particular, regulation of micronutrient zinc deficiency and tolerance to excess metals in extremophile hyperaccumulator plant species. Following a careful selection process Dr. Ana Gonçalves Leite de Assunção was selected. Dr. Assunção holds a PhD in Ecology and Ecotoxicology of Plants from the Free University of Amsterdam, The Netherlands. She has worked as researcher and project coordinator (NWO-VENI laureate) at the Laboratory of Genetics at Wageningen University, the Netherlands, and at the Department of Plant Biology and Biotechnology at University of Copenhagen, Denmark. She uses physiological, genetic, genomic and molecular biology approaches to study the molecular basis and regulation of micronutrient homeostasis network in the model plant species Arabidopsis as well as in Arabidopsis-related metal hyperaccumulator species. Over the past years Dr. Assunção has built a solid network in this field. For details regarding the project activities during her contract period, please see final periodic report.
Position 3. Following an agreement with the EU Project Officer the initial position of an experienced scientist was changed to an Executive Coordinator position for CIBIO centre. After a careful recruitment process a decision was made to hire Dr. Ana Natália Domingues Dias for this position. Dr. Dias holds a PhD in Marine Ecology from the University of Algarve, and has solid research experience in ecology, biology and evolutionary ecology from a top Environmental Sciences School (School of Environmental Sciences, University of East Anglia, UK) and the University of Valencia. She brought along solid expertise in coordination of large scale international collaboration in research and post-graduation education involving a top world university (MIT) and all the main Portuguese universities; coordination and management of complex administrative tasks; advanced communication skills, namely: communication with a large network of researchers, students and faculty; communication and marketing strategies for managing international recruitment of students and researchers; communication of research and educational achievements to governmental bodies, media and general public; interaction with Portuguese higher education stake holders and main research funding bodies; interaction and communication with companies and other institutions. Project report via link in the final periodic report.
All of the above-indicated researchers have had a great impact on the Next Generation Sequencing related research in their field of Science at CIBIO. Their expertise have specifically strongly enhanced the speed and efficiency with which the Next Generation Sequencing as well as the “Genomics factory” has been implemented.
Twinning: Expertise and know-how exchange, and Training for knowledge transfer to CIBIO
Background
The twinning (Expertise and know-how exchange, and Training for knowledge transfer) in the CIBIO-New-Gen project was divided into two Work packages (WP5 and WP6). WP5 was dedicated to Principal Investigators and/or experienced staff from CIBIO to be engaged in two-sided visits with European and other international research centers of excellence in specific areas of interest, in order to assure a flow of knowledge to CIBIO. The twinning activities had the character of short-term scientific missions, allowing for a regular exchange of scientists from our institution with institutes abroad, aiming to maximize impact and quality of our research. WP6 was primarily devoted to training CIBIO’s more junior or early career researchers, to foster mobility during their education and optimize their gain of knowledge and technological skills from supporting partners and other EU centers of Excellence. This WP was composed by both short and long term training missions. An additional aim was, for both work packages, to strengthen already ongoing partnerships as well as to promote the establishment of new collaborations during the duration of the project and beyond.
The Twinning activities under both WP5 and WP6 did suffer a significant delay as described in the periodic reports. Following the agreed extension of the NewGen project with the EC, the activities have been more effectively planned and the resources extensively explored. Some of the initially planned Twinning activities had to be reprogrammed or even changed to a different twinning partner due to the delay of the project. In total almost 30 training and mobility activities (WP5) have been executed during the project period, involving PI´s and/or experienced staff. Some of these activities had the form of two-sided visits to/from European and other international research centers of excellence in specific areas of interest related to WP5 (for further description see the two periodic reports and in the specific individual deliverable report D6). In other cases where it was not possible to plan in a two-sided twinning within the NewGen project time lines, the CIBIO researcher has performed the visit to the supporting institute, bringing back the much needed know-how to CIBIO for continuous set up and protocol improvement of the installed Next Generation Sequencing platform. In the latter cases a visit from a researcher from the supporting partner institution is planned in and will be supported by other project resources. Eleven junior or early stage career researchers were involved in these Training and mobility activities (WP6), the majority of which being in the form of long term training for effective knowledge transfer to CIBIO which is crucial both when it comes to the implementation of new Next Generation Sequencing approaches/services as well as application of complex downstream data analysis techniques. These Training and Mobility activities that have been executed during the course of the CIBIO-New-Gen project are described in more detail in the specific Deliverable report D8 as well as in the periodic reports.
As indicated above the visits have focused mainly on Next Generation Sequencing techniques implementation, protocol set-up as well as the downstream sequence data analyses methodologies. The exchange and twinning activities also served for an improved integration of CIBIO in the European Research Area, through long lasting partnerships with research groups in Europe and America.
CIBIO-INBIO had a network of research collaborations across Europe and America that was heavily consolidated and expanded through an exchange of know-how and expertise program on several important research areas using Next Generation Sequencing (NGS), through the NEWGEN project, outlined below:
a) Conservation Genetics and Wildlife Management
• Collaboration with Max Planck Institute (Germany) in completing the sequencing of mitochondrial genome of 236 of the sable antelope - Department of Evolutionary Genetics – Advanced DNA Sequencing Techniques.
• Collaboration with the University of Montana (US) regarding analyses of transcriptome sequencing and expression data generated using Next Generation Sequencing technologies in the context of the study of genetic bases of adaptive traits and gene expression - Good Lab – Evolutionary Genomics, Department of Ecosystems and Conservation Sciences.
• Collaboration with Cornell University (US) related to ongoing and future collaborative projects with the main goal of developing a protocol for genomic analysis (Genotyping by Sequencing – GBS) of museum and non-invasive samples - Department of Ecology and Evolutionary Biology.
• Collaboration with the University of São Paulo (Brazil) regarding overall exchange of expertise and limitations using genomics in the field of conservation genetics - Department of Genetics and Evolutionary Biology, Institute of Bioscience (IB).
• Collaboration and cooperation with the University of California Los Angeles (US), on the genome resequencing and analysis of the grey wolf in Europe. This involved both genomics training for the CIBIO-INBIO collaborators as well as development of new pipelines for genomic analysis - Department of Ecology and Evolutionary Biology.
b) Human Evolutionary Genetics
• Collaboration with Max Planck Institute (Germany) in the field of Evolutionary Anthropology.
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c) Tropical Biology
• Collaboration with the Museu Paraense Emílio Goeldi, Federal University of Pará (Brazil), with the focus on implementing a protocol for target capture and massively parallel sequencing of ultra-conserved DNA elements (UCEs) for comparative studies on Neotropical rainforest bird species with shallow evolutionary time scales.
• Joint efforts with Universidade Estadual Paulista (UNESP), Brazil, regarding the development and optimization of a Restriction site Associated DNA sequencing (RADseq) method for three species of Neotropical toads belonging to the Rhinella marina species group.
d) Ecology and Evolution of Aquatic Organisms
• Collaboration with Oxford University focusing on training exchange and discussing future research collaboration and potential application of genome and transcriptome studies to future research lines - Department of Zoology.
• Collaboration with the Romberg Tiburon Center (RTC), California (US) focusing on knowledge transfer, namely on the sequencing of the transcriptome of individuals of the limpet Pattela vulgata.
e) Immunogenetics, Microbes and Infectious Diseases
• Strengthening of existing collaboration with the Swedish Agricultural University, Uppsala (Sweden), regarding metagenomics applications and downstream bioinformatics analysis - Viral Metagenomics and Bioinformatics Group.
• Collaboration with ANSES - French Agency for Food, Environmental, Occupational Health and Safety, Ploufragan (France) focusing on NGS applications in the studies of the rabbit hemorrhagic disease virus (RHDV).
f) Biodiversity of Deserts and Arid Regions
• Collaboration with Virginia Polytechnic Institute and State University (US) and the University of California, Berkeley (US) on the transcriptomics of Salamandra salamandra - Department of Horticulture (Virginia Polytechnic and State University) and the Department of Environmental Science (UC Berkeley).
• Collaboration with the University of Oulu (Finland) focusing on training and collaborative research on genomic signal of ecological diversification and transcriptomic tools applied to behavioral and morphological traits - Department of Biology.
• Collaboration with the University of Jyvaskyla (Finland) in the development of transcriptomic tools for studying behavioral and morphological traits (this collaboration will also be extended to the University of Leipzig).
g) Plant Biology
• Collaboration with the Claude Bernard University, Lyon (France) on genomic characterization of grapevine (Vitis vinifera) cultivars namely, for the identification and comparative evolutionary analysis of specific genes families, such as stilbene synthases, which are important for wine chemical profile and organoleptics - Sex and Evolution Team, Biometrics and Evolutionary Biology Laboratory. This collaboration is paramount to the CIBIO-INBIO’s ongoing research effort to perform genomic characterization of National grapevine varieties, through NGS to resequencing of grapevine genomes.
h) The Applied Ecology
• Collaboration with the Imperial College London (UK) on linking metagenomics and land-use changes. This included the planning for a joint project application regarding this topic in Iberia in a forthcoming call - Forest Ecology and Conservation Research Group.
i) The Applied Phylogenetics – AP group
• Research exchange with the Center for Conservation & Evolutionary Genetics (CCEG), part of the Smithsonian Conservation Biology Institute (SCBI) and based at the National Zoological Park (NZP) of the Smithsonian Institution, US, with the aim to a) develop human resources by means of training in NGS laboratory methods, b) generate genomic datasets for three main research projects in applied phylogenetics, and c) to develop bioinformatics skills by means of a planned workshop at CIBIO-INBIO by researchers of CCEG and SI.
j) Environmental Archaeology and Livestock Genomics and Conservation
• Collaboration with University of California, Davis (US) focusing on knowledge transfer of restriction-site associated DNA sequencing (RADSeq) method, which samples at reduced complexity across target genomes, and promises to deliver high resolution population genomic data - Department of Animal Science.
• Research exchange with Uppsala University (Sweden) to enable CIBIO-INBIO researchers to learn more about the means of collection and analysis of genomic datasets, namely the analysis and assembly of historic cattle and wheat genomes - Ancient DNA laboratory Evolutionary Biology Centre (EBC).
k) The Population Genetics, Hybridization and Speciation
• Collaboration with Uppsala University (Sweden) focusing on several lines of research associated with the mapping of multiple traits of both wild and domestic rabbits. The group in Uppsala is a world-leader in animal genetics and uses both domesticated and natural populations for genetic dissection of simple and complex traits. This collaboration will extend to other animal groups - Functional genomics in domestic animals group (PI: Leif Andersson)
Benefits/Project impact
In addition to what has been outlined above regarding the impact of the CIBIO-New-Gen project, there are additional and extremely important benefits to be reported. Due to CIBIO´s long-standing collaboration and twinning activities, CIBIO was approved to become the first LIA (Laboratoire International Associé) of CNRS (Centre National de la Recherche Scientifique, France) in Portugal. This will be a twinning between CIBIO and Montpellier, France, and is a unique achievement for CIBIO as an institute as well as for Portugal. The EC funded CIBIO-New-Gen project and the implemented NGS platform had profound impact in this CNRS decision. CIBIO has also created the concept of TwinLabs in Portugal, and opened the first one in Angola in October 2012. We are now in the process of negotiating TwinLabs in Morocco, Brazil, and the USA. In great part due to the CIBIO-New-Gen project and the new Genomics Platform, as well as to the well-defined Twinning and Training programs, our PhD Program in Biodiversity, Genetics and Evolution (BIODIV) secured the largest funding given by FCT to any PhD program in the country, all fields. The BIODIV funding is composed by two components: i) the first is a series of 48 PhD scholarships, and ii) the second is a series of 16 PhD scholarships, exclusive for Angolan citizens aiming to develop their research. In total, this corresponds to an amount of 4.5 M€ investment in training awarded to CIBIO. Altogether, this is exactly what would be expected by a CAPACITIES project: capacity building at CIBIO, and is demonstrating that CIBIO is becoming a prestigious international player in its field.
Workshops, conferences, dissemination and visibility
Background
This WP was devoted to the broadening and facilitation of exchange of scientific experience and expertise of CIBIO, as well as to making knowledge available to the general public and the society as a whole.
Updating CIBIO´s website/Implementation of the dedicated CIBIO New-Gen project website
The new CIBIO’s website as well as a CIBIO New-Gen project dedicated website were implemented in the final reporting period. The brand new and extensively improved CIBIO website (http://cibio.up.pt/) was put on-line in September 2014, and a dedicated CIBIO-New-Gen project website (http://cibio-newgen.pt) was soon after linked to this main site. Specific details (and reference to the CIBIO-New-Gen project) were also made available on the CIBIO main website at (http://cibio.up.pt/ctm-molecular-analysis-services) with a link to the specific project website. The CIBIO-New-Gen project website has been continuously updated regarding project activities/news as well as new sequencing services being provided.
Organization of international workshops, national meetings and courses
The international workshops, national meetings and courses organized during the course of the CIBIO-New-Gen project are outlined below. More specific details regarding the meetings were given in the individual Deliverable reports.
1. The Advances in Ecological Speciation (AES) Conference
April 29-30, 2013 | Auditorium - Vairão Campus
The AES conference aims at joining researchers and students from all over the world to present and discuss cutting-edge ecological speciation research. The aim is to provide an informal but stimulating scientific atmosphere, which promote strong interaction and brainstorming between students and more experienced researchers.
The conference included 5 invited plenary talks, 16 oral communications, poster sessions and a round table covering the topics of parallel adaptation, genomics of ecological speciation, adaptive radiations and hybridization, among others.
2. PlantUp - CIBIO Info Meeting
September 16, 2014 | Auditorium - Vairão Campus
This Info Meeting (all in Portuguese) was organized in the context of the CIBIO-New-Gen project and included all the research groups at the University of Porto performing research in plant biology. The meeting consisted of an opening presentation regarding the CIBIO-New-Gen project and the status of the platform installation as well as services provided. This was followed by individual scientific presentations from the respective plant biology groups and concluded with a discussion. Around 60 researchers participated. For the official meeting program, see the individual Deliverable report D11/12.
3. XI CONGRESS OF THE PORTUGUESE ETHOLOGICAL SOCIETY
October 9-10, 2014 | Auditorium - Vairão Campus
CIBIO hosted the 11th Congress of the Portuguese Ethological Society, on the 9th and 10th of October 2014. SPE congresses attract most researchers and students working on animal behaviour in Portugal, and are an opportunity to meet leading international invited speakers. The congress covers all research areas in animal behaviour, and talks are given in English. This congress highlights the emerging area of behavioural genetics, with two invited speakers from this area: Nadia Aubin-Horth (Université Laval, Québec) and Adam Jones (Texas A&M University). Invited speaker Marta Moita (Champalimaud Neuroscience Programme, Lisbon) will talk about neuroscience of fear, and László Garamszegi (Estación Biológica de Doñana, Seville) about phylogenetic meta-analyses of behaviour.
4. TiBE 2015 – Global Biodiversity Change – from Genes to Ecosystems
1st and 2nd June 2015 | Auditorium - Vairão Campus
The TiBE 2015 conference provided a broad perspective on recent advances in the study of the ecological impacts of social and economic drivers, land-use dynamics, biological invasions, species range and niche dynamics, genetic structure and flow, and other dimensions of change in ecosystems, landscapes and their biodiversity. Furthermore the conference allowed a direct link with applied ecology including: i) the detection, interpretation and forecast of changes in a given territory; ii) the anticipation of trends in the patterns of drivers of ecological change, and the early detection of biodiversity responses and ecosystem changes; and iii) the support to model-assisted frameworks for cost-efficient conservation and monitoring. The program included four scientific sessions, each with a plenary conference by an invited international expert and several communications proposed by the conference participants.
5. GENOMICS SEMINAR/WORKSHOP
June 18-19, 2015 | Auditorium - Vairão Campus
A 2–day Genomics Seminar/Workshop was organized in the context of the CIBIO-New-Gen project, and being part of a complete Genomics Week at the institute (see also under organized courses/workshops below). During these two days, five major topics in genomics research in the area of Next Generation Sequencing were covered:
1. Environmental Genomics;
2. Phylogenomics;
3. Conservation/Population Genomics;
4. AgriGenomics;
5. One Health Genomics.
6. Next Generation Sequencing Info Afternoon @ CIBIO-InBIO
September 30, 2015 | Auditorium - Vairão Campus
This Next Generation Sequencing (NGS) information afternoon included presentations from CIBIO researchers as well as by researchers from other Portuguese research centers, and covered the following NGS application projects: The Cork Oak sequencing project, AgriGenomics, Using NGS to understand genome reticulation and adaptive phenotypes challenged by climate change, Conservation and evolutionary genomics of the shad species, Alosa alosa (Savél) and A. fallax (Savelha) in Portugal and throughout Eurasia, and Marine Genomics. This was also the official conclusion of the CIBIO New-Gen project as well as the kick-off session for the ERA Chair in Environmental Metagenomics, EnvMetaGen – Horizon 2020 –WIDESPREAD awarded to CIBIO in 2015. A number of companies, representatives from the University of Porto, FCT (the Portuguese national funding agency for science, research and technology), as well as representatives and researchers from other research institutes attended the event. There were around 80 participants in total. The official meeting program is presented on the individual Deliverable report D11/12.
In addition to the above described workshops and meetings, a number of courses were also organized in the scope of the CIBIO-New-Gen project. These courses are outlined below and described in more detail in the Deliverable report D11/12:
1. WORKSHOP GENOTYPING-BY-SEQUENCING (GBS): USES AND ABUSES May 30, 2014 | Vairão Campus
Genotyping-by-Sequencing (GBS) is potentially a very useful technique for genotyping model and non-model organisms quickly and cheaply at many thousands of loci simultaneously. However, the technique is relatively new and specific considerations and biases are starting to emerge. In this workshop, Thomas White (Cornell University, USA and Canterbury Christ Church University, UK) described how to conduct a GBS analysis, from tissue collection to bioinformatics analysis. Tom highlighted some of the potential pitfalls on the way, and possible solutions.
2. WORKSHOP 'INTRODUCTION TO RAD DATA ANALYSIS September 24-26, 2014 | Vairão Campus
This was a three-day course by Dr. Alan Brelsford, Univ. Lausanne, which covered the following topics:
1. Introduction to Unix command-line environment
2. De-multiplexing and quality control of raw sequence data
3. Analysis of GBS/RAD data without a reference genome using Stacks
4. Analysis of GBS/RAD data with a reference genome using Bowtie/Samtools
5. Export and quality filtering of raw genotypes using Vcftools
3. ADVANCED COURSE GENOTYPING BY SEQUENCING (GBS): PRINCIPLES, APPROACHES AND APPLICATIONS June 15-17, 2015 | Vairão Campus
This aim of the course was to give attendees a broad overview of Genotyping-by-Sequencing (GBS), including the principles of how data are obtained by the various different approaches, and their advantages and disadvantages. A question and answer session helped to determine the right approach for different study systems or special cases, such as degraded DNA. There were also practical data-analysis sessions, where attendees were guided through example data processing with various analysis tools.
4. INTRODUCTION TO NEXT-GENERATION SEQUENCING DATA AND ANALYSIS COURSE
June 23-26, 2015 | Vairão Campus
This course provided an introduction to the basics of next generation sequencing data and analysis, and includes hands-on exercises throughout.
Topics covered include:
1. Basics of the Linux command line;
2. DNA/RNA preparation and sequencing technologies, including reduced-representation sequencing;
3. What to do with newly-delivered sequencing data;
4. Assembling sequences of varying sizes and complexities;
5. Variant discovery;
6. Annotation of small to large datasets;
7. Ancient and variable-coverage DNA;
8. Transcriptomes and gene expression analysis; and
9. Walkthroughs of example analyses.
Emphasis throughout was on understanding fundamentals, and on developing skills for design of practical sequencing projects and analysis of sequencing data in light of research questions and biological and practical limitations.
TV documentaries
The production of the series of 13 TV-documentaries on biodiversity has been concluded and resulted in a unique project of science dissemination. Negotiations have so far been concluded with the Portuguese first TV channel RTP1. The series of documentaries will be broadcasted on prime time, substituting a high profile BBC Nature series. Each documentary is briefly outlined below:
1. Crocodiles in the deserts of Mauritania
A group of biologists investigates the biology of crocodiles isolated in mountain oases of the Sahara, in Mauritania. The genetic analysis of collected samples allows the analysis of population connectivity and differentiation. The episode describes the work of senior biologist José Carlos Brito and twining with different Universities in Spain, Morocco and Mauritania.
2. The expansion of cashew plantations in Guinea-Bissau
In the last decades the plantations of cashew have been expanding considerably in Guinea-Bissau, substituting the native forest or rice, the basic food of people. This episode follows the impact of cashew plantations in biodiversity, economy and Guinean society, through the research work of Luís Catarino, and twinning with local institutions and the Tropical Biology Institute (IICT).
3. Investigating cooperative breeding in birds in South Africa
Social weavers live in large communities and build huge nests in the trees of southern Kalahari, South Africa. Research in cooperative breeding in birds analyses the behaviour of social weavers, in particular seeking to understand the role of helpers during the breeding season. This episode follows the work of biologist Rita Covas, and twinning with local institutions, and the Universities of Montpellier (France) and Sheffield (UK).
4. Using tree-frogs to understand the evolution of the Atlantic Forest (Brasil)
The movements of a group of species with low vagility can help to understand the evolution of the habitats in which they occur. In this episode, the study of tree-frogs included in the genus Phyllomedusa is exemplified in order to reconstruct the evolution of the Brasilian Atlantic Forest. This is the work of biologist Fernando Sequeira, and twinning with the Universities of São Paulo (USP), Federal do Pará (UFP) and Estadual de São Paulo (UNESP), all in Brazil.
5. Portugal: an European hotspot of bat diversity
Bats represent about 25% of mammals in the planet. This episode relates how research has been increasing knowledge on the more than 20 species occurring in Portugal, and helping conservation programs. This work is headed by biologist Hugo Rebelo, and includes the development of new capture techniques as well as twinning with the University of Bristol (UK) and the Doñana Biological Station (Seville, Spain).
6. Distribution and characterization of the reptiles from Cape Verde
The genetic analyses of reptile species in all islands of the Cape Verde archipelago allowed the correction of old classification mistakes and suggested new distribution maps. This knowledge is of crucial relevance for the conservation and reserve planning in the country. This episode follows the research of Raquel Vasconcelos and twinning with local institutions.
7. São Tomé e Príncipe: the highest rate of bird endemism in the world
When a population of a species is split in two and the groups are no longer in contact, they generally follow different and divergent evolutionary trajectories, adapting to different habitats. This project aims to understand this process using the birds of São Tomé e Príncipe (Gulf of Guinea, Africa) as a model system. This episode follows the work of biologist Martim Melo, and twinning with local and South-African institutions.
8. Conservation of migratory fish species in Europe
Migratory anadromous fish feed and grow in the sea, but spawn in freshwater. Due to the construction of dams in most European rivers, some populations were able to adapt to freshwater and exhibit a sedentary lifecycle. This episode follows the research of Paulo Alexandrino and seeks to understand the evolutionary and genetic mechanisms which allowed this process. Twinning with different institutions in France and Italy is described.
9. Conservation genetics of intriguing sloth species in Brasil and Panama
Sloths live in the tropical forests of Central and South America. Recent deforestation in the Amazon and Atlantic Forest is a serious threat to this group of unique species. Using genetic tools, researchers aim to understand the consequences of forest fragmentation on the conservation programs of sloths. This episode follows the work of biologist Nadia Moraes-Barros and twinning with Brazilian and European institutions.
10. Understanding human admixture in the Cape Verde islands
Using one of the most admixed human populations in the planet, it was possible to better understand the genetic mechanisms which are responsible for eye and skin pigmentation. In addition, genetic data allowed the reconstruction of the colonization history of the archipelago. This episode describes the work of biologist Jorge Rocha, and twinning with the Universities of Cabo Verde, Stanford (USA), and the Max-Planck Institute (Leipzig, Germany).
11. Following the steps of terrible invader: the cane toad
A group of Portuguese and Brazilian researchers is reconstructing the evolutionary and adaptation history of the cane toad, starting in its native distribution area, the Amazon, to the recent and uncontrolled invasion of the Australian territory. This episode follows the research of biologist Fernando Sequeira and twinning with both Brasilian (Universidade Federal do Pará) and Australian Universities (Universities of Townsville and Melbourne).
12. Recovery and conservation of the Purple Gallinule in the Mediterranean
The purple gallinule is an iconic bird from the Mediterranean. While in the Roman period it was considered as an ornamental bird and depicted in mosaics all over the Mediterranean, in more recent times was almost driven to extinction due to human persecution. This episode follows the work of Ricardo Lopes who, using molecular and ecological tools, has inspired reintroductions and conservation programs in different European countries.
13. Understanding the history of domestication
Domestication of animals and plants changed completely the history of human societies, and is also the major experiment ever made in biology. Rabbits are the only species domesticated in Western Europe, and offer a unique model to better understand the molecular bases underlying domestication. This episode follows the research of Nuno Ferrand and melts genomics with French medieval history, from monasteries to modern Museums.
Publication of booklets
Two booklets disseminating the information about the current Next Generation Sequencing project activities at CIBIO have been produced. The titles of the two booklets are indicated below:
1. Next Generation Sequencing projects at CIBIO-InBIO – Conservation and Metagenomics
2. Next Generation Sequencing projects at CIBIO-InBIO – Evolution
(ISBN - ISBN - 978-989-99518-0-8)
Participation of CIBIO´s researchers in high-level international conferences
Seventeen participations by CIBIO researchers at 10 different high-level international conferences have taken place during this final periodic reporting period. The list of conference participations is outlined in the individual Deliverable report D13. The 10 different high-level conferences attended are listed below:
1. Cordon Research Conference in Speciation 2015, Ventura, USA
2. Botany 2015, Edmonton, Alberta, Canada
3. The Viral Hepatitis Congress 2015, Kap Europa, Frankfurt, Germany
4. SMBE 2015 –Society for Molecular Biology and Evolution, Vienna, Austria
5. 6th International Barcode of Life Conference 2015, Guelph, Canada
6. ESEB 2015 | European society for evolutionary biology 2015, Lausanne, Switzerland
7. 6th Congress of European Microbiologists (FEMS 2015), Maastricht, The Netherlands
8. The 2nd Microbe R&D and Business Collaboration Forum Europe, London,
9. Evolution 2015, Guarujá, Brazil
10. 7th European Congress of Mammalogy, Stockholm University, Sweden
Organization of Seminars including FP7 encouragement topic and establishment of consortia
The seminars organized within the context of the CIBIO-New-Gen project under the course of the project are outlined below. These seminars were disseminated widely and were open for researchers from other scientific institutes, companies with interest in the scientific field as well as the general public:
1. John Archer, CIBIO-InBIO/UP - Involved in the establishment of a Bioinformatics unit at CIBIO SLAYING THE CHIMERA IN VENOM GLAND TRANSCRIPTOMICS - January 21, 2015
2. Antonio Muñoz, CIBIO-InBIO/UP – Involved in the establishment of a Bioinformatics unit at CIBIO RETROSPECTIVE OF MY WORK IN BIOINFORMATICS: SQUEEZING DATA TO GET INFORMATION - January 30, 2015
3. Lee Ann Rollins, Deakin University, Australia - INVASIVE SPECIES AS A MODEL FOR THE STUDY OF RAPID EVOLUTION - July 20, 2015
4. Tomas Larsson, University of Gothenburg, Sweden - DE NOVO SEQUENCING OF “UNCONVENTIONAL” SPECIES - PROMISES, PROGRESS AND PITFALLS - June 29, 2015
5. Courtney Hofman, Center for Conservation and Evolutionary Genetics, Smithsonian Institution & University of Oklahoma's Laboratories of Molecular Anthropology and Microbiome Research, USA - ARCHAEOGENOMICS IN THE ANTHROPOCENE - September 28, 2015
6. Love Dalén, Swedish Museum of Natural History, Sweden - USING ANCIENT GENOMES TO EXAMINE POPULATION DEMOGRAPHY, DIVERGENCE AND GENETIC STOCHASTICITY - September 21, 2015
In the context of the impact and benefits of the NewGen project, InBIO/CIBIO has become a partner of a recently approved FCT Research Infrastructure, GenomePortugal, as well as the leading/coordinating Institution for a second approved FCT Research Infrastructure, PORBIOTA.
GenomePortugal is a distributed genome sequencing and analysis RI for basic/applied genome research and advanced services. Its main objectives are: i) potentiate the participation of Portuguese scientists in national and international genome projects and ii) develop clinical, environmental, marine and agrofood genomics, biotechnology and green chemistry. GenomePortugal congregates the national research centers involved in genomic research, brings over 3 million euros of investment in DNA sequencing and analysis instruments, over 40 researchers and technical personnel, and important bioinformatics expertise dispersed across a wide geographical area, under the umbrella of a professionally managed RI.
PORBIOTA is a research infrastructure, which aims to collect, store and manage all kinds of biodiversity data from the entire Portuguese territory. It will be connected to LIFEWATCH, which is its European counterpart. PORBIOTA will promote a national agenda on biodiversity survey and research, providing services to the administration, the scientific community, and society. The consortium includes top national research centres, natural history museums, the Portuguese node of GBIF, the LTER Portugal network, ICOS Portugal, the Azorean Biodiversity Portal, and the Nature Conservation and Forests institute (ICNF). The direct impact and connection from the CIBIO-New-Gen project to/and from PORBIOTA is through the powerful data analysis platform implemented in the New-Gen project (additional data processing and storage power will be purchased through the PORBIOTA project to upgrade the existing platform).
In connection to this WP7 task a project application (Project entitled “EnvMetaGen – Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics”) was submitted by CIBIO within the scope the European Commission call Horizon 2020-WIDESPREAD-2104-2, extensively utilizing the NGS platform implemented during the CIBIO-New-Gen project. The project was approved and was initiated in September this year, with a kick off meeting organized jointly with the concluding meeting of the New-Gen project (September 30, 2015).
Society/Industry/SMEs info days and impact
A number of combined scientific and Next Generation Sequencing platform information days, open to researchers, companies and the public in general, have been organized as also outlined above: i) An info day for researchers and groups at the University of Porto performing research in the area of plant biology. The meeting consisted of an opening presentation regarding the CIBIO-New-Gen project and the status of the platform installation as well as services provided. This was followed by individual scientific presentations from the respective plant biology groups; ii) A two-day Genomics Seminar/Workshop, being part of a complete Genomics week at the institute. The two days involved seminars with both a research approach and commercial touch (in the areas of Environmental Genomics, Phylogenomics, Conservation/Population Genomics, AgriGenomics and One Health Genomics) and were open to scientists, companies and the general public; and iii) a Next Generation Sequencing Info Afternoon (also serving as the conclusive meeting for the CIBIO-New-Gen project), involving a closing/status presentation regarding the CIBIO-New-gen project, but also specific presentations regarding Next Generation Sequencing applications of ongoing projects. The meeting was open for the general public, researchers and companies. A number of companies and institutions/organizations were invited and among those present were representatives from EDP (a leading company in the energy sector in Portugal), Stab-Vida (a Portuguese biotech/genetics company), University of Porto (represented by the Vice-Dean, Maria João Ramos), FCT (the Portuguese national funding agency for science, research and technology), INIAV (State Laboratory related to the Agricultural Research and Veterinarian Science), and CCMAR (Research Centre from the University of Algarve).
The impact of the above mentioned meetings (as well as the additionally organized meetings and seminars indicated further above) was great. We have had a number of service requests/collaboration proposals from other research institutes, governmental organizations (e.g. the Portuguese National Institute for Health), and a number of hospitals. Some of these activities are already ongoing and others are currently being planned.
In addition, we continue our collaboration with StabVida regarding commercialization of services related to genetics and are in negotiations regarding collaborations on Next Generation Sequencing service provision.
CIBIO is presently concluding discussions with a French Biotech company, ANTAGENE, that is interested in opening a company (a subsidiary or more likely a separate company with strong connections to ANTAGENE) together with CIBIO (collaboration regarding NGS services). ANTAGENE is a biotechnology company specialized in providing services in the area of DNA analysis (domestic and wild animals) and the idea is to expand this service portfolio using the broad expertise CIBIO has, developments made by the institute’s researchers, and the implemented NGS and data analysis platform (CIBIO-New-Gen project). In this first phase the plan is to establish the new company in Portugal and the rest of the Iberian Peninsula in the areas of: a) Bovine Selection, b) Wildlife genetics (in both Europe and Africa), c) Environmental DNA (e.g. Fresh water quality, soil quality/component etc), as well as d) Current ANTAGENE services in DNA testing for certification of origin and disease prevention. The new company will initially be based at the CIBIO facilities at the University of Porto campus in Vairão. The intention and aim is to employ personnel holding a PhD for positions in the areas of commercialization, implementation of novel DNA tests, scientific management within the company, as well as for the applied research and development.
CIBIO has furthermore ongoing collaboration protocols and support with/from EDP – “Energias de Portugal, S.A.” in the area of biodiversity and is also coordinating a REN Chair in Biodiversity (co-sponsored by REN – National Energy Networks and FCT - the Portuguese national funding agency for science, research and technology).
CIBIO-New-Gen project Impact and Benefits
Further to the CIBIO-New-Gen project impact described above it should also be mentioned that in the last couple of years, the project coordinator has been responsible for the building of a project to fully recover the old Museum of Natural History and Science of the University of Porto. We were successful in getting a grant from Structural Funds through the Northern Region of Portugal of over 4.5 M€ to prepare the new Hall of Biodiversity in one of the most iconic and symbolic houses of Porto, the Andresen House. Financial support was also provided from the Vice-Dean of the University of Porto. This is paving the way for winning the organization of ECSITE 2017 in Porto, joining more than 1300 people from all over the world working in Scientific Museums and Centres. Benefiting from this situation, dissemination of science for the general public will be a joint activity involving both CIBIO and the Natural History and Science Museum of the University of Porto.
Potential Impact:
The CIBIO-New-Gen project allowed CIBIO to strengthen significantly its research profile and potential, raising its capacity to establish collaborations both at national and international levels. The acquisition of the most powerful next generation genome sequencer in Portugal and the extensive interchange program for students and researchers allowed the institute to upgrade its research and computing infrastructure and to train its staff in new cutting edge methodologies used in the emerging area of genomics. All of this turned the institute much more attractive for researchers and research institutions. This capacity is most relevant not only for attracting new talent and collaborations but also for retaining talent, reversing brain drain, and developing into higher levels existing collaborations. Through the CIBIO-New-Gen project, CIBIO became a stronger player both in the Portuguese research system and in the European Research Area. Below we will give more detail on various impacts of the project.
Better integration of CIBIO in the European Research Area, through long lasting partnerships with research groups in Europe and America
CIBIO has a network of research collaborations across Europe and America that was consolidated and expanded through an exchange of know-how and expertise program on several important research areas using Next Generation Sequencing (NGS), through the CIBIO-New-Gen project.
a) Conservation Genetics and Wildlife Management
• Collaboration with Max Planck Institute (Germany) in completing the sequencing of mitochondrial genome of 236 of the sable antelope - Department of Evolutionary Genetics – Advanced DNA Sequencing Techniques.
• Collaboration with the University of Montana (US) regarding analyses of transcriptome sequencing and expression data generated using Next Generation Sequencing technologies in the context of the study of genetic bases of adaptive traits and gene expression - Good Lab – Evolutionary Genomics, Department of Ecosystems and Conservation Sciences.
• Collaboration with Cornell University (US) related to ongoing and future collaborative projects with the main goal of developing a protocol for genomic analysis (Genotyping by Sequencing – GBS) of museum and non-invasive samples - Department of Ecology and Evolutionary Biology.
• Collaboration with the University of São Paulo (Brazil) regarding overall exchange of expertise and limitations using genomics in the field of conservation genetics - Department of Genetics and Evolutionary Biology, Institute of Bioscience (IB).
• Collaboration and cooperation with the University of California Los Angeles (US), on the genome resequencing and analysis of the grey wolf in Europe. This involved both genomics training for the CIBIO-INBIO collaborators as well as development of new pipelines for genomic analysis - Department of Ecology and Evolutionary Biology.
b) Human Evolutionary Genetics
• Collaboration with Max Planck Institute (Germany) in the field of Evolutionary Anthropology.
c) Tropical Biology
• Collaboration with the Museu Paraense Emílio Goeldi, Federal University of Pará (Brazil), with the focus on implementing a protocol for target capture and massively parallel sequencing of ultra-conserved DNA elements (UCEs) for comparative studies on Neotropical rainforest bird species with shallow evolutionary time scales.
• Joint efforts with Universidade Estadual Paulista (UNESP), Brazil, regarding the development and optimization of a Restriction site Associated DNA sequencing (RADseq) method for three species of Neotropical toads belonging to the Rhinella marina species group.
d) Ecology and Evolution of Aquatic Organisms
• Collaboration with Oxford University focusing on training exchange and discussing future research collaboration and potential application of genome and transcriptome studies to future research lines - Department of Zoology.
• Collaboration with the Romberg Tiburon Center (RTC), California (US) focusing on knowledge transfer, namely on the sequencing of the transcriptome of individuals of the limpet Pattela vulgata.
e) Immunogenetics, Microbes and Infectious Diseases
• Strengthening of existing collaboration with the Swedish Agricultural University, Uppsala (Sweden), regarding metagenomics applications and downstream bioinformatics analysis - Viral Metagenomics and Bioinformatics Group.
• Collaboration with ANSES - French Agency for Food, Environmental, Occupational Health and Safety, Ploufragan (France) focusing on NGS applications in the studies of the rabbit hemorrhagic disease virus (RHDV).
f) Biodiversity of Deserts and Arid Regions
• Collaboration with Virginia Polytechnic Institute and State University (US) and the University of California, Berkeley (US) on the transcriptomics of Salamandra salamandra - Department of Horticulture (Virginia Polytechnic and State University) and the Department of Environmental Science (UC Berkeley).
• Collaboration with the University of Oulu (Finland) focusing on training and collaborative research on genomic signal of ecological diversification and transcriptomic tools applied to behavioral and morphological traits - Department of Biology.
• Collaboration with the University of Jyvaskyla (Finland) in the development of transcriptomic tools for studying behavioral and morphological traits (this collaboration will also be extended to the University of Leipzig).
g) Plant Biology
• Collaboration with the Claude Bernard University, Lyon (France) on genomic characterization of grapevine (Vitis vinifera) cultivars namely, for the identification and comparative evolutionary analysis of specific genes families, such as stilbene synthases, which are important for wine chemical profile and organoleptics - Sex and Evolution Team, Biometrics and Evolutionary Biology Laboratory. This collaboration is paramount to the CIBIO-INBIO’s ongoing research effort to perform genomic characterization of National grapevine varieties, through NGS to resequencing of grapevine genomes.
h) The Applied Ecology
• Collaboration with the Imperial College London (UK) on linking metagenomics and land-use changes. This included the planning for a joint project application regarding this topic in Iberia in a forthcoming call - Forest Ecology and Conservation Research Group.
i) The Applied Phylogenetics – AP group
• Research exchange with the Center for Conservation & Evolutionary Genetics (CCEG), part of the Smithsonian Conservation Biology Institute (SCBI) and based at the National Zoological Park (NZP) of the Smithsonian Institution, US, with the aim to a) develop human resources by means of training in NGS laboratory methods, b) generate genomic datasets for three main research projects in applied phylogenetics, and c) to develop bioinformatics skills by means of a planned workshop at CIBIO-INBIO by researchers of CCEG and SI.
j) Environmental Archaeology and Livestock Genomics and Conservation
• Collaboration with University of California, Davis (US) focusing on knowledge transfer of restriction-site associated DNA sequencing (RADSeq) method, which samples at reduced complexity across target genomes, and promises to deliver high resolution population genomic data - Department of Animal Science.
• Research exchange with Uppsala University (Sweden) to enable CIBIO-INBIO researchers to learn more about the means of collection and analysis of genomic datasets, namely the analysis and assembly of historic cattle and wheat genomes - Ancient DNA laboratory Evolutionary Biology Centre (EBC).
k) The Population Genetics, Hybridization and Speciation
• Collaboration with Uppsala University (Sweden) focusing on several lines of research associated with the mapping of multiple traits of both wild and domestic rabbits. The group in Uppsala is a world-leader in animal genetics and uses both domesticated and natural populations for genetic dissection of simple and complex traits. This collaboration will extend to other animal groups - Functional genomics in domestic animals group (PI: Leif Andersson)
Upgrading the RTD capacity and capability of CIBIO as well as the quality of research carried out by CIBIO.
A large part of our research lines requires DNA level analysis of biological diversity. During the last years new technologies arose, and now the trend is to look at whole genomes or part of genomes: the genomics era has arrived. To be able to accompany the fast development of this new and important area and develop state of the art research and education we had the necessity to acquire additional research capacity for analysis, which was possible through the NEWGEN Project. With this project we could buy the most advanced next-generation sequencing platform in the country, recruit experienced researchers and train our staff and students in the new techniques to produce and handle NGS data. Genome sequencing generates an extraordinary amount of data, which require highly specialized professionals, larger computing capacity, namely storage and analytical capacity for downstream sequence analysis and for modelling approaches. All of this we could achieve with the NEWGEN project. In addition to purchasing the NGS platform, we upgraded our computing capacity and we created a new research team of bioinformaticians who have been giving a huge support to the other researchers in the institute in moving to the new era of genomics. As an example, in the last national call for research grants of FCT (National Foundation for Science and Technology), all the 82 research proposals submitted by our researchers involved NGS methods and the bioinformatics researchers were part of the research teams of all the projects. As a result, we had a success rate of 23% compared to a national average success rate of 13%.
Improved research capacity for increased contribution to regional economic and social development
Before the CIBIO-New-Gen project, Portugal as a whole, and the North convergence region in particular, did not possess a core next-gen sequencing facility and the associated bioinformatics for conducting state of the art genomics analysis. With the implementation of CIBIO-next-gen, we were able to provide these resources and give the region and the country the opportunity to integrate these new technologies into the research and education systems.
We increased the capacity of CIBIO to provide services to regional and national authorities, companies and other research centres and we are presently able to provide a number of specific NGS services, which is an important asset for the sustainability of the Centre and also to the socio-economic development of the North region. Becoming a highly specialized scientific and technological service provider, raised the prestige and technological profile of the institute and of the region. The number of NGS services clients is steadily increasing, currently including the National Health Institute (INSA) and a number of national research centres and institutes.
In addition, the CIBIO-New-Gen project helped CIBIO to attract and retain excellent professionals, allowing us to counteract the brain drain which has been affecting severely the North region and Portugal as whole, over the last years, due to the economic crisis. This centre has increased the number of researchers with a PhD during the CIBIO-NewGen project: in 2011 the centre had 137 researchers with a PhD and in 2015 it has 164.
Research infrastructure establishment
The technological capacitation by CIBIO-New-Gen was paramount for CIBIO to be an important player on the recently created Portuguese Roadmap for Research Infrastructures. In this context CIBIO is currently leading the Portuguese E-Infrastructure for Information and Research on Biodiversity – PORBIOTA, and is an active member of two other infrastructures: National Facility for Genome Sequencing and Analysis – GenomePortugal, and Portuguese Research Infrastructure of Scientific Collections – PRISC.
The purpose of the PORBIOTA infrastructure is to collect and manage biodiversity data from across the country and promote a national agenda of monitoring and research in biodiversity and provide services to the scientific community, policy makers, managers and the general public. PORBIOTA hopes to contribute to increase public awareness of the importance of biodiversity and improve scientific culture through science programs for citizens and other popular science programs. The infrastructure is managed by a consortium that includes top national research units, with significant experience in research in biodiversity and in the development of computer-supported technologies, natural history museums, the Portuguese node of GBIF (Global Biodiversity Information Facility), and the National Authority for Nature and Forest Conservation (ICNF). The infrastructure will be integrated into LIFEWATCH (ESFRI), the European e-infrastructure for research on biodiversity and ecosystems.
GenomePortugal is a distributed infrastructure for genome sequencing. Its main objectives are: i) to enhance the participation of Portuguese scientists in national and international projects in genomics and, ii) to develop clinical genomics, environmental, marine and food processing, biotechnology and environmental chemistry. GenomePortugal brings together national research centers involved in genome sequencing spread across a wide geographical area and is expected to put Portugal on the map of countries with technological capacity and experience to sequence complex genomes and to involve our scientific community in the genomics revolution currently underway. The main lines of action of this distributed infrastructure are: a) to develop a cadre of very specialized staff to operate installed instruments and to analyze data and simultaneously, improving computational power and bioinformatics tools; b) to provide high standards of training in NGS analysis, through the organization of Summer Schools and Workshops, microarray and bioinformatics methodologies, open to national and international students and researchers; and c) sequencing genomes of scientific and economic relevance to Portugal. This infrastructure is of strategic relevance because genome sequencing and analysis is fueling a major revolution in the biological, biomedical, environmental, agrofood and marine sciences, with visible impact on biotechnology, green chemistry, management of natural resources and health. By building the research capacity and aligning its research strategy with the Regional, National and European development priorities for the 2015-2020 period, GenomePortugal will make measurable contributions to regional development, the national economy and to retain highly qualified human resource.
PRISC is a research infrastructure focusing on the conservation, study and accessibility of Portuguese scientific collections. PRISC will provide the present and future Portuguese scientific collections high standards of preservation conditions, inventory and accessibility to allow them to be increasingly used for scientific research, postgraduate education and the promotion of scientific culture in Portugal, and will support directly the development of research and innovation in all areas of sciences and humanities through increased use of Portuguese scientific collections.
Involvement in regional Authorities and Private entities
CIBIO is deeply involved with regional authorities and private companies in the assessment, minimization and compensation of the environmental impacts of large infrastructure development, such as road infrastructures, railway lines, power distribution networks, and dams. CIBIO-INBIO’s activity thus contributes for the sustainable regional development, by providing solutions, which blend the needs of social and economic development with that of environmental protection. This includes the scientific analysis of environmental impacts and technical design of compensatory mitigation frameworks, as well as the development of scientifically sound monitoring programs. This work is carried out by two autonomous units in the institute: Centre for Molecular Analysis (CTM) and Centre for Studies and Projects in Applied Ecology (GEPE). While CTM is dedicated to applied research on the evaluation and use of animal and plant genetic resources, GEPE provides services in biodiversity conservation and monitoring. Both units work on technology transfer and develop partnerships with private national and foreign companies and governmental bodies. In addition, we have a program of Invited Research Chairs co-funded by FCT and large industry partners: a) EDP Biodiversity Chair (power production and distribution systems); b) Infrastructures of Portugal Biodiversity Chair (roads and railway lines); and c) REN in Biodiversity Chair (energy transmission systems).
CIBIO provides many services and customized research for industry. Currently we have contracts with 22 different companies. We were asked by a biotechnology French company, Antagen, to create a Portuguese branch for them, Antagene Portugal.
The improvement of our research capacities has increased our contributions to the sustainable regional development, by fostering the application of novel knowledge and techniques to the practical solution of critical environmental problems. This includes, for instance, the increasing use of genetic tools in impact assessment, non-invasive monitoring of animal populations, and analysis of difficult to study population processes such as dispersal, among other applications.
Improvement of participation of CIBIO in FP7 projects and H2020
During the CIBIO-New-Gen project the participation of CIBIO in European research projects has increased compared to previous years. This was translated into five grants from FP7 and four from H2020 framework programs. These projects have brought 3.6 M € to the institute.
Particularly, we would like to highlight the ERA Chair granted in early 2015. The Era Chair application ‘Capacity Building at CIBIO for Research and Innovation Using Environmental Metagenomics’ (Acronym: EnvMetaGen) was based on the increased research capacity in gene sequencing CIBIO acquired through the CIBIO-New-Gen project and was funded by the EU with 2,4 M€. The project aims to expand the research and innovation potential of CIBIO through the creation of an ERA Chair in Environmental Metagenomics. The goal is to strengthen the research potential of human resources, lab facilities and next-generation genome sequencing equipment, supporting an emerging research line in environmental metagenomics for applications in biodiversity conservation, invasive species control, ecosystem services assessment, and environmental (bio)monitoring. The EnvMetaGen is allowing us to launch an international tender for hiring a top researcher as well as her/his team in order to promote adequate critical mass in the area of environmental metagenomics. It is expected that this area of research will have an impact both at regional, national and European level, creating innovative and low cost approaches and methodologies for the study of biodiversity, ecology and environmental quality.
Furthemore, CIBIO has been developing other important research collaborations with international partners. In 2014 we created the International Associated Laboratory (LIA) ‘Biodiversity and Evolution’ with a focus on biodiversity and evolutionary biology. The LIA established a formal cooperation between the Centre National de la Recherche Scientifique (CNRS), the Université Montpellier 2 Sciences et Techniques (UM2), the Institut de Recherche pour le Développement (IRD), the École Pratique Hautes Études (EPHE), France, and CIBIO-INBIO, the University of Porto and the Portuguese Science and Technology Foundation (FCT), built upon several well established collaborations between CIBIO and the French research units. In 2013 our researcher Rui Figueira created, and leads since then, the Portuguese Node of GBIF (Global Biodiversity Information Facility). CIBIO-INBIO is the leader of the research e-infrastructure ‘PORBIOTA’, created in 2015, which will collect, store and manage all biodiversity data from the Portuguese territory and will be connected to its European counterpart LIFEWATCH. PORBIOTA includes, among other members, LTER Portugal, the Portuguese node of LTER (Long-Term Ecological Research Network of sites where long term ecological investigation is carried out) and ICOS Portugal, the Portuguese node of ICOS (Pan-European research infrastructure for Integrated Carbon Observation System). We are also formal members of the EUBON project (Building the European Biodiversity Observation Network) and participate in several collaborative research networks funded by COST Actions.
Sustainability of the measures beyond the project lifetime
CIBIO has several contracts with enterprises and other public and private entities in the areas of ecological inventory and monitoring, biodiversity management and conservation with special interest for game management, environmental impact assessment and natural resources valorization. Excellence in research and renovated capacity, as well as the new bioinformatics capacity allowed us to seek for more sustainability measures and new sponsors to our research. For instance, this year we have made a research contract with REN (major company of energy transmission systems) and FCT, for a 3 years research chair which funds the salary and research of a senior researcher (total of 480.000€). Also this year we negotiated the extension of the research chair with Infrastructures of Portugal (large road and railway company) for two additional years (160.000€). This chair supports the salary of a senior researcher and three post-docs.
CIBIO is presently concluding discussions with the French Biotech company ANTAGENE, about opening a company (a subsidiary or more likely a separate company with strong connections to ANTAGENE). ANTAGENE is a biotechnology company specialized in providing services in the area of DNA analysis (domestic and wild animals) and they wish to expand this service portfolio using the broad expertise of CIBIO in this field, namely recent technical developments made by our researchers, which involve the NGS and data analysis platform (NewGen). In this first phase the plan is to establish the new company in Portugal to reach the rest of the Iberian Peninsula in the areas of: a) bovine delection, b) wildlife genetics (in both Europe and Africa), c) environmental DNA (e.g. fresh water quality, soil quality/component etc), and d) current ANTAGENE services in DNA testing for certification of origin and disease prevention. The new company will initially be based at CIBIO facilities. We plan to employ personnel with a PhD degree for the areas of commercialization, implementation of novel DNA tests, scientific management, and applied research and development.
During 2015 we have also signed several contracts for assessing and following up environmental impacts in the construction of important human-made structures at national level, such as windmill farms, dams and linear structures (roads and rail trains). This work includes the proposal of minimization and compensation measures, inventory and characterization of fauna, including vertebrates and invertebrates, flora and habitats of terrestrial, freshwater and coastal ecosystems, monitoring programs for endangered plant and animal populations located in areas affected by human-made structures and development and validation of new methodologies used in wildlife management and ecological monitoring.
Commercialization of services provided by CIBIO´s Centre for Molecular Analysis (CTM) together with the ongoing collaboration with the Biotech/Genetics company StabVida provide an important and regular income for the centre.
Dissemination of knowledge and spreading of excellence
The improvement of public appreciation and understanding of biodiversity and evolutionary biology is a priority mission of CIBIO. Our researchers are actively committed into a diversified range of science dissemination and outreach initiatives.
During the CIBIO-New-Gen project the following activities were performed:
A large numbers of international workshops, national meetings and courses have been organized during the course of the CIBIO-New-Gen project and in the context of science dissemination and outreach initiatives: The Advances in Ecological Speciation (AES) Conference (April, 2013), PlantUp – CIBIO Next Generation Sequencing Info Meeting (September, 2014), the XI Congress Of The Portuguese Ethological Society (October, 2014), the TiBE 2015 – Global Biodiversity Change – from Genes to Ecosystems conference (June, 2015), the Genomics Seminar/Workshop (June, 2015), Next Generation Sequencing Info Afternoon @ CIBIO-InBIO, (September, 2015), and the Next Generation Sequencing workshops/courses: Workshop Genotyping-By-Sequencing (GBS): Uses And Abuses (May, 2014), Workshop 'Introduction To Rad Data Analysis (September 24-26, 2014), Advanced Course Genotyping By Sequencing (GBS): Principles, Approaches And Applications (June 15-17, 2015), Introduction To Next-Generation Sequencing Data And Analysis Course (June 23-26, 2015).
TV documentaries
A production of a number of TV-documentaries on biodiversity has been concluded and has resulted in a unique project of science dissemination. Negotiations have so far been concluded with the Portuguese first TV channel RTP1. The series of documentaries will be broadcasted on prime time.
Publication of booklets
For further develop its current activities, CIBIO will strengthen meetings with science journalists, to promote communication links and attain successful science dissemination. Along these lines 2 booklets have been produced regarding, i) Next Generation Sequencing Projects at CIBIO-INBIO – Conservation and Metagenomics, and ii) Next Generation Sequencing Projects at CIBIO-INBIO – Evolution
Society and Industry info days and establishment of partnerships
A number of combined scientific and Next Generation Sequencing platform information days, open to researchers, companies and the public in general, have been organized as also outlined above: i) An info day for researchers and groups at the University of Porto performing research in the area of plant biology. The meeting consisted of an opening presentation regarding the CIBIO-New-Gen project and the status of the platform installation as well as services provided. This was followed by individual scientific presentations from the respective plant biology groups; ii) A two-day Genomics Seminar/Workshop, being part of a complete Genomics week at the institute. The two days involved seminars with both a research approach and commercial touch (in the areas of Environmental Genomics, Phylogenomics, Conservation/Population Genomics, AgriGenomics and One Health Genomics) and were open to scientists, companies and the general public; and iii) a Next Generation Sequencing Info Afternoon (also serving as the conclusive meeting for the CIBIO-New-Gen project), involving a closing/status presentation regarding the CIBIO-New-gen project, but also specific presentations regarding Next Generation Sequencing applications of ongoing projects. The meeting was open for the general public, researcher and companies. A number of companies and institutions/organizations were invited and among those present were representatives from EDP (a leading company in the energy sector in Portugal), Stab-Vida (a Portuguese biotech/genetics company), University of Porto, FCT (the Portuguese national funding agency for science, research and technology), INIAV (State Laboratory related to the Agricultural Research and Veterinarian Science), and CCMAR (from the University of Algarve). These activities in combination with the extensive Twinning and know-how transfer/exchange activities outlined above have strengthened ongoing collaborations and paved the way for new partnerships.
After the conclusion of the CIBIO-New-Gen project, we anticipate that the many hired researchers will continue to strengthen CIBIO’s research excellence, since major efforts for sustainability will most surely lead to a growth environment and expansion.
It should be stated in the end here that the dissemination will continue through courses, conference organization as well as conference participation and scientific publications (important to note is that many more publications are in the pipeline and will come out after the conclusion of the project – delay of project and the set-up of the platform to produce data for publication caused this delay).
List of Websites:
http://cibio-newgen.pt/homepage
http://cibio.up.pt/
Prof. Nuno Ferrand ICETA - Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Porto, Portugal
Tel.: +351252660411
Email: cibio.up@cibio.up.pt
The work of CIBIO-New-Gen project was divided into 8 different Work Packages. A summary of the achievements regarding those Work Packages for the entire project period is outlined below:
Acquisition and implementation of a Next Generation Sequencing platform and recruitment of experienced researchers
Implementation of the high and medium throughput/output platform unit at CIBIO
A high and medium throughput/output sequencing platform was implemented at the CIBIO facilities. The selected Illumina HiSeq 1500 and the Illumina benchtop MiSeq sequencers were installed in September 2013. The acquisition also included a variety of support equipment to make the NGS workflow complete and fully functional. Following the implementation of the platform, a period of in-house test runs and protocol implementations were performed. CIBIO is currently able to provide a number specific NGS and downstream data analyses services both internally at the institute as well as nationally in Portugal (see NewGen website for service information – http://cibio-newgen.pt/).
Recruitment of experienced researchers
The employment of two experienced researchers with extensive experience in the area of sequencing by synthesis as well as data analysis was fulfilled. After a thorough recruitment process the first selected candidate was Dr. Nadia de Moraes Barros. Dr. Barros holds a PhD in Genetics and Evolutionary Biology (Biosciences Institute, University of S. Paulo, Brazil). The second selected candidate was Dr. Filipe Jorge Garret Vieira. Dr. Vieira has a PhD in Biological Sciences (University of Barcelona, Spain), as well as Post-Doc experience at UC Berkeley, USA, with a special emphasis on Next-Generation Sequencing (NGS) data.
Improvement of data analysis capacity at CIBIO & initiation and implementation of a bioinformatics group
Acquisition of a “Genomics Factory”: computer capacity and software
A data storage and a linked powerful computing cluster was acquired and implemented. The choice fell an a Isilon X400 (x3) data storage unit with the capacity of up 108 TB, and a computing/server cluster consisting of 5 nodes (one computer with 1 TB RAM, 4 processors, 8C and four computers with 256 GB RAM, 4 processors, 8C. One node of the four smaller computers was installed at the CIBIO site in Vairão, and the Isilon storage unit and the rest of the computing cluster was installed at one of University of Porto´s (UP) data centers. The overall acquisition process and the implementation was guided and advised by Dr. Nuno Fonseca (EBI, Cambridge, UK), Dr. Filipe Vieira, who was hired as a research scientist for the CIBIO-New-Gen project, and who decided to accept a job offer at the Natural History Museum of Denmark, and the two bioinformaticians (see below) hired towards the end of 2014. CIBIO is currently able to provide a number of NGS application services as well as complex data analysis support.
Recruitment of two Bioinformaticians and three Research Scientist
Recruitment of two bioinformaticians with expertise in Bioinformatics, Computational biology and Next Generation Sequencing data analysis
Following a thorough selection procedure the two positions were filled with the following researchers:
Dr. Antonio Muñoz - Dr. Munñoz holds a PhD in Computational Biology and Bioinformatics. He brings along a solid expertise in data analysis as well as software development from a large variety of different projects ranging from fruit quality determination, olive transcriptome assembly and annotation, as well as hospital connected biomedical projects, and Dr. John Archer - Dr. Archer holds a PhD in computational biology from the University of Manchester, UK and brings along expertise in analysis of NGS data, statistics, algorithm development, software development, recombination analysis, sequence alignment and phylogeny. During his PhD he developed and implemented the first NGS read mapper capable of mapping reads derived from highly variable data sources such as rapidly evolving RNA viral populations.
High-skilled research scientist recruitment
Three Post-Doc fellows were recruited (see below), all were very well integrated at CIBIO and developed their work as expected. However, we had to re-recruit/replace the holder of Position 1 two times since the contract holders decided to explore other carrier opportunities during the contract period.
Selected candidates:
Position 1. Dr. Wen-Ya Ko - Dr. Ko holds a PhD in Biology (Molecular Evolutionary Biology option), Pennsylvania State University, USA. He has a very solid expertise regarding both experimental and theoretical approaches including DNA and phenotypic/clinical data collection in the field, molecular biology experiments in laboratory, computational programming for data analysis, and development of statistical tools for identifying signatures of evolutionary adaptation in the human genome.
Position 1 - replacement/re-recruitment (for Dr. Ko)
Dr. Daniel Vasco - Dr Vasco holds a PhD in Mathematical Biology from the University of Texas, and he brought along extensive expertise in the areas of Programming, Bioinformatics data analysis (Large-scale (massive) next generation data analysis and critical assessment, relational data bases (my SQL), SNP and microarray data, genomic signal analysis), Applied mathematics, computational modeling and statistics (stochastic simulation, algorithm testing and evaluation, algorithm development and implementation on multiple platforms), as well as Matched experimental and computational protocols for single-cell genomics and transcriptomics.
Position 1 - replacement/re-recruitment (for Dr. Vasco)
Dr. Magda Gaya - Dr. Gaya holds a PhD in Human Population Genetics from the University of Barcelona and brings along extensive expertise in comparative and functional genomics related to Human polymorphic inversions and Molecular evolution, Biomedical Bioinformatics – Adaptive evolution in the human lineage, and functional analysis of genomes, among other skills.
Position 2. Dr. Ana Assunção - Dr. Assunção holds a PhD in Ecology and Ecotoxicology of Plants from the Free University of Amsterdam, The Netherlands. She has worked as researcher and project coordinator (NWO-VENI laureate) at the Laboratory of Genetics at Wageningen University, the Netherlands, and at the Department of Plant Biology and Biotechnology at University of Copenhagen, Denmark.
Position 3. Dr. Natália Dias - Dr. Dias holds a PhD in Marine Ecology from the University of Algarve, and has solid research experience in ecology, biology and evolutionary ecology from a top Environmental Sciences School (School of Environmental Sciences, University of East Anglia, UK) and the University of Valencia. She brought along solid expertise in coordination of large-scale international collaboration in research and post-graduation education involving a top world university (MIT) and all the main Portuguese universities
Twinning: Expertise and know-how exchange, and Training for knowledge transfer to CIBIO
In total almost thirty training and exchange activities (WP5) and eleven know-how transfer and mobility activities (WP6) have been executed during the project period, involving PI´s, other experienced staff as well as junior or early stage career researchers. The visits have focused mainly on Next Generation Sequencing techniques implementation, protocol set-up as well as the downstream sequence data analyses methodologies. The exchange and twinning activities also served for an improved integration of CIBIO in the European Research Area, through long lasting partnerships with research groups in Europe, as well as with American partner institutions, and several important research areas in the context of Next Generation Sequencing have been/are being addressed.
Workshops, conferences, dissemination and visibility
Updating CIBIO´s website/Implementation of the dedicated CIBIO New-Gen project website
A new CIBIO’s website as well as a CIBIO-New-Gen project dedicated website were implemented and the websites have been continuously updated regarding project activities/news as well as new sequencing services being provided throughout the project.
Conference participation and Organization of international workshops, national meetings and courses
Seventeen participations by CIBIO researchers at 10 different high-level international conferences have taken place and numerous international workshops, national meetings and courses have been organized during the course of the CIBIO-New-Gen project as outlined in the report and deliverables. These activities have had a huge impact regarding the opportunities for researchers from a large number of research groups at CIBIO to disseminate and discuss their scientific results and findings at these different venues and events.
TV documentaries
A production of a series of TV-documentaries on biodiversity has been concluded and resulted in a unique project of science dissemination. The series of documentaries will be broadcasted in the Portuguese first TV channel RTP1 on prime time.
Publication of booklets
Two booklets disseminating the information about the current Next Generation Sequencing project activities at CIBIO have been produced. The booklets cover NGS approaches in the fields of Conservation, Metagenomics and Evolution.
Organization of Seminars including FP7 encouragement topic and establishment of consortia
6 seminars have been organized within the context of the CIBIO-New-Gen project under the course of the project. These seminars were disseminated widely and were open for researchers from other scientific institutes, companies with interest in the scientific field as well as the general public.
In the context of the impact and benefits of the NewGen project here, CIBIO has become a partner of a recently approved FCT (National Foundation for Science and Technology) Research Infrastructure, GenomePortugal, as well as the leading/coordinating Institution for a second approved FCT Research Infrastructure, PORBIOTA.
Society/Industry/SMEs info days and impact
A number of combined scientific and Next Generation Sequencing platform information days, open to researchers, companies and the public in general, have been organized. The impact of the mentioned meetings (as well as the additionally organized meetings and seminars) was great. We have had a number of service requests/collaboration proposals from other research institutes, governmental organizations (e.g. the Portuguese National Institute for Health), and a number of hospitals. Some of these activities are already ongoing and others are currently being planned.
In addition, we continue our collaboration with StabVida regarding commercialization of services related to genetics and are in negotiations regarding collaborations on Next Generation Sequencing service provision.
CIBIO is also in conclusive negotiations with representatives from a French biotech company (ANTAGENE), regarding establishing a spin-off company at the CIBIO campus in Vairão (collaboration regarding NGS services and applications).
CIBIO has furthermore ongoing collaboration protocols and support with/from EDP – “Energias de Portugal, S.A.” in the area of biodiversity and is also coordinating a REN Chair in Biodiversity (co-sponsored by REN – National Energy Networks and FCT - the Portuguese national funding agency for science, research and technology).
Project Context and Objectives:
The focus of research at CIBIO is evolutionary biology, conservation genetics, and ecology in a conservation context. A large part of research lines employs the DNA level analysis of biological diversity. During the last years, new technologies arose in this field, which provide today the opportunity to generate new types of datasets with especially high information content for genome based investigation of biological diversity. The CIBIO- New-Gen proposal has two main objectives: 1) to install New Generation sequencing platforms and integrate the respective techniques in CIBIO scientists research, and 2) to equip the unit with the computer infrastructure necessary to handle the increasing amount of data and analytical procedures for downstream sequence analysis and for modeling approaches. This activity will be accompanied by strengthening our research staff and by training and exchange of expertise in collaboration with international partners. The acquisition and implementation of the new technologies and the development of the respective expertise will enable the institution to fully develop its potential in quality of research and international recognition.
As indicated above the CIBIO unit intents through this REGPOT project to strengthen its impact on a regional and international scale by using an integrated approach that involves the acquisition of research equipment to remain internationally competitive, the acquisition of additional expertise to implement this equipment, the intensification of dissemination activities to foster its international recognition and to further reinforce its involvement in regional and national stakeholder activities.
Moreover, an overall objective is also to ensure that CIBIO becomes a full participant of the European Research Area (ERA), reinforces its excellence and creativity and be able to take advantage of the knowledge and know-how existing in high ranking institutions in Europe (e.g. the MPI for evolutionary anthropology and Uppsala University) and the USA (e.g. University of California, Berkeley), all of them world leading research organizations. With the implementation of this project, CIBIO’s active contribution to the regional economy and social welfare will be significantly increased.
Project Results:
Project objectives and description of main S & T results
Description of the overall Project objectives
The focus of research at CIBIO is evolutionary biology, conservation genetics, and ecology in a conservation context. A large part of research lines employs the DNA level analysis of biological diversity. During the last years, new technologies arose in this field, which provide today the opportunity to generate new types of datasets with especially high information content for genome based investigation of biological diversity. The CIBIO-New-Gen project had two main objectives: 1) to install New Generation sequencing platforms and integrate the respective techniques in CIBIO’s research, and 2) to equip the unit with the computer infrastructure necessary to handle the increasing amount of data and analytical procedures for downstream sequence analysis and for modeling approaches. These activities were accompanied by strengthening our research and by training staff and exchanging expertise in collaboration with international partners. The acquisition and implementation of the new technologies and the development of the respective expertise enabled the institution to develop its potential research quality and international recognition.
CIBIO intended, through this REGPOT project, to strengthen its impact at a regional and international scales by using an integrated approach involving the acquisition of research equipment to remain internationally competitive, the acquisition of additional expertise to implement this equipment, the intensification of dissemination activities to foster its international recognition and to further reinforce its involvement with regional and national stakeholders.
Moreover, an overall objective was also to ensure that CIBIO becomes a significant participant in the European Research Area (ERA), reinforcing its excellence and creativity and being able to take advantage of the knowledge and know-how existing in world leading research institutions in Europe (e.g. the MPI for evolutionary anthropology and Uppsala University) and US (e.g. University of California, Berkeley).
The results of the CIBIO-New-Gen project allowed CIBIO to strengthen significantly its research profile and potential, raising its capacity to establish collaborations both at national and international levels. The acquisition of the most powerful next generation genome sequencer in Portugal and the extensive interchange program for students and researchers allowed the institute to upgrade its research and computing infrastructure and to train its staff in new cutting edge methodologies used in the emerging area of genomics. All of this turned the institute much more attractive for researchers and research institutions. This capacity is most relevant not only for attracting new talent and collaborations but also for retaining talent, reversing brain drain, and developing into higher levels existing collaborations. Through the CIBIO-New-Gen project, CIBIO became a stronger player both in the Portuguese research system and in the European Research Area.
The work of CIBIO-New-Gen project was divided into 8 different Work Packages. The achievements regarding those Work Packages for the entire project period are reported below:
Acquisition and implementation of a Next Generation Sequencing platform and recruitment of experienced researchers
Implementation of the high and medium throughput/output platform unit at CIBIO
According to the objectives of WP1 and 2, a high and medium throughput/output sequencing platform were implemented at CIBIO facilities. The selected Illumina HiSeq 1500 (plus the cBot device) and the Illumina benchtop MiSeq sequencers were installed in September 2013. This reversible-terminator sequencing by synthesis technology (TruSeq chemistry) based system features two run modes, rapid run and high output run mode, providing a flexible and scalable platform that supports a broad range of applications and study sizes such as Targeted resequencing, gene expression, whole-genome sequencing and epigenetics. As indicated, HiSeq 1500 system also features the cBot, a stand-alone automated system that creates clonal clusters from single molecule DNA templates. The acquisition also included a variety of support equipment to make the Next Generation Sequencing workflow complete and fully functional.
Following the implementation of the platform, a period of in-house test runs and protocol implementations were performed with the aim of setting up the Next Generation Sequencing (NGS) services properly. CIBIO is currently able to provide a number specific NGS and downstream data analyses services both internally at the institute as well as nationally in Portugal. A number of recently concluded, as well as still ongoing sequencing, projects have been performed/are being executed, involving a wide range of taxonomic groups of organisms such as mammals, birds, reptiles, fish, several invertebrates and plants: Brindle rabbit, Plumage color canary, Singing varieties canary, Palanca (giant sable antelope), Littorina (sea snails), Hares, Human, Alosa (shad), Scorpions, Deer, and Wine (see NewGen website for service information – http://cibio-newgen.pt/). The Next Generation sequencing services currently implemented and provided are: Whole genome sequencing, RNA-seq, RAD sequencing, Transcriptome sequencing and Metagenomics sequencing
Recruitment of experienced researchers
The employment of two experienced researchers with extensive experience in the area of sequencing by synthesis as well as data analysis was fulfilled. After a thorough recruitment process the first selected candidate was Dr. Nadia de Moraes Barros. Dr. Barros holds a PhD in Genetics and Evolutionary Biology (Biosciences Institute, University of S. Paulo, Brazil). She worked as a postdoctoral researcher at the Laboratory of Evolutionary Biology and Vertebrate Conservation (Labec, IB-USP, Brazil). Her research focus is on conservation genetics in Neotropics and she brings along experience in phylogeography, phylogeny, comparative morphological analyses, population genetics and the use of Next Generation Sequencing in selecting molecular markers for endangered and non-model species.
The second selected candidate was Dr. Filipe Jorge Garret Vieira. Dr. Vieira has a PhD in Biological Sciences (University of Barcelona, Spain), as well as Post-Doc experience at UC Berkeley, USA, with a special emphasis on Next-Generation Sequencing (NGS) data. Here he was focusing on two main topics: i) the development of Next Generation Sequencing methods for the analysis of low coverage/quality data; and ii) the study of rice domestication to better understand its origin and dissemination.
Dr. Barros is still contracted at CIBIO and Dr. Vieira has moved to a new position at the University of Copenhagen.
Impact as a result of the CIBIO-New-Gen project (applying to the 2 above described Work packages)
As a direct impact of the CIBIO-New-Gen funding CIBIO was able to seek and get approval of substantial additional funding in the context of capacity building through Next Generation Sequencing. Examples of additional achieved funding are:
1) GenomePortugal (National Facility for Genome Sequencing and Analysis; CIBIO is a member of this FCT funded Research Infrastructure). GenomePortugal is a distributed genome sequencing and analysis RI for basic/applied genome research and advanced services, and the network covers all research centers and governmental institutes with NGS equipment in Portugal.
2) CIBIO – Genomics, Biodiversity and Evolution – funding from the ON2 Programme, by the Regional Governmental body CCDR-n, from Structural funds - consumables and additional small laboratory equipment related to major sequencing projects currently performed at CIBIO (for example the full and de novo sequencing of the Giant Sable Antelope genome from Angola, an animal in the brink of extinction, and with global visibility, which is the national symbol of Angola).
3) Additional funds for a series of research contracts and post-doctoral positions were granted by the National Foundation for Science and Technology (FCT). These successful proposals, strongly benefitted from this project as they will be all using the new NGS and bioinformatics platform.
Improvement of data analysis capacity at CIBIO & initiation and implementation of a bioinformatics group
The objectives were to recruit a Head for a new Bioinformatics Core group followed by the installation of the “Genomics Factory” supervised by the new Head. As described in the mid-term report, these Tasks could not been performed as planned and within the first set timelines, but a solution/deviation for making progress regarding this crucial work package was achieved during the final reporting period (see below).
Acquisition of a “Genomics Factory”: computer capacity and software
We were not able to hire a person for the position of Head of the Core Bioinformatics group under this work package, but an agreement was made with the selected top candidate for the position, Dr. Fonseca (EBI, Cambridge, UK) to work as an advisor in the process of the Genomics Factory acquisition and implementation. Similarly, Dr. Garett Vieira, who was hired as a research scientist (with specific NGS bioinformatics expertise, see above), and who decided to accept a job offer at the Natural History Museum of Denmark (University of Copenhagen), also agreed to continue to provide expert advice after his move to Denmark. The two bioinformaticians hired towards the end of 2014 were also heavily involved in the implementation process of the overall Genomics Factory, in particular regarding the final installations of the data storage unit and the computing server clusters. Regarding the purchase process of the Data Storage and the linked computing cluster, an official tender process was performed and following a thorough selection process with an important involvement by the team of advisors/consultants mentioned above, the choice fell on purchasing an Isilon X400 (x3) data storage unit with the capacity of up 108 TB, and a computing/server cluster consisting of 5 nodes (one computer with 1 TB RAM, 4 processors, 8C and four computers with 256 GB RAM, 4 processors, 8C. One node of the four smaller computers was installed at the CIBIO site in Vairão, and the Isilon storage unit and the rest of the computing cluster was installed at one of University of Porto´s (UP) data centers (at the Faculty of Sciences). The latter installation is giving us access to UPs experienced technical/maintenance team as well as direct connection/access to additional storage capacity and computing clusters already existing at this site. The overall NGS and bioinformatics platform is up and running and we have already performed a number of sequencing projects and downstream bioinformatics data analyses. We have, in addition, organized several courses/workshops making use of the installed data analysis equipment and software.
Impact as a result of the CIBIO-New-Gen project overall and specifically the improvement of the bioinformatics capacities at CIBIO
As a result of the CIBIO-New-Gen project and here specifically the installation and implementation of the powerful data computing and storage equipment, CIBIO was able to earn a series of extremely important additional funds which put our research centre in a very competitive position both nationally and in the European Research Area (ERA).
CIBIO is the leader institute and the CIBIO-New-Gen Coordinator is the PI for a National Consortium/Research Infrastructure (RI), PORBIOTA (the Portuguese E-Infrastructure for Information and Research on Biodiversity), which is in the future expected to become the Portuguese node of the European ESFRI LifeWatch. This Research Infrastructure is funded by the Portuguese Foundation for Science and Technology and the funding covers additional computing and storage power, as well as resources for hiring researchers and technicians to work within the data analyses workflow resulting from massive sequencing projects using our Genomics Platform facility.
In addition we were also able to recruit two skilful bioinformaticians, forming the primary structure of a well-needed bioinformatics group at CIBIO (more details below under recruitment). Our intension is to expand this group, by hiring bioinformatics technicians and researchers, e.g. via the above indicated PORBIOTA research infrastructure funding.
Recruitment of two Bioinformaticians and three Research Scientist
Background
As indicated in the mid-term report, the recruitment objectives for this work package had at that time been fulfilled except for the recruitment of the Principal Investigator for Computational and Theoretical Biology. For this position, and in the context of the difficulties in employing senior researchers in the areas of bioinformatics and computational biology, it was agreed with the EC (the project officer) to split this position into two positions for slightly less senior bioinformatics, computational biology and NGS data analysis positions.
Specific advertisements for the experienced research and bioinformatics positions (see below) were published in scientific journals of high circulation and visibility, mobility networks like EraCareers, Euraxess, and Marie Curie Fellowships association, social networks as well as via e-mailing to international research partners and collaborators.
Recruitment of two bioinformaticians with expertise in Bioinformatics, Computational biology and Next Generation Sequencing data analysis
Following a thorough selection procedure the two positions were filled with the following researchers:
Dr. Antonio Muñoz - Dr. Munñoz holds a PhD in Computational Biology and Bioinformatics. He brings along a solid expertise in data analysis as well as software development from a large variety of different projects ranging from fruit quality determination, olive transcriptome assembly and annotation, as well as hospital connected biomedical projects. For further details on Dr. Muñoz background as well the NewGen project activities he has been involved in, please see his NewGen activity report link in the final periodic report.
and
Dr. John Archer - Dr. Archer holds a PhD in computational biology from the University of Manchester, UK and brings along expertise in analysis of NGS data, statistics, algorithm development, software development, recombination analysis, sequence alignment and phylogeny. During his PhD he developed and implemented the first NGS read mapper capable of mapping reads derived from highly variable data sources such as rapidly evolving RNA viral populations. His postdoctoral research was driven by national and international collaborations, involving investigations regarding the emergence of drug resistance mutations within HIV-1 populations as well as the development of a viral genotyping tool. He has furthermore developed an assembly tool capable of assembling of non- chimeric contigs from read datasets harbouring isoform variation, being the first such tool that successfully archives this task. For further details on Dr. Archers background as well the NewGen project activities he has been involved in please, see his NewGen activity report link in the final periodic report.
High-skilled research scientist recruitment
Three Post-Doc fellows were recruited (see below), all were very well integrated at CIBIO and developed their work as expected. However, we had to re-recruit/replace the holder of Position 1 two times since the contract holders decided to explore other carrier opportunities during the contract period.
Selected candidates:
Position 1. Dr. Wen-Ya Ko - Dr. Ko holds a PhD in Biology (Molecular Evolutionary Biology option), Pennsylvania State University, USA. He has a very solid expertise regarding both experimental and theoretical approaches including DNA and phenotypic/clinical data collection in the field, molecular biology experiments in laboratory, computational programming for data analysis, and development of statistical tools for identifying signatures of evolutionary adaptation in the human genome. Dr. Ko decided to leave CIBIO because he had an offer of a tenure track faculty position in his home country (Taiwan). Please see the activity report during his contract period (link in final periodic report).
Position 1 - replacement/re-recruitment
Following a careful selection procedure to substitute Dr. Wen-Ya Ko, a decision was made to hire Dr. Daniel Vasco. Dr Vasco holds a PhD in Mathematical Biology from the University of Texas, and he brought along extensive expertise in the areas of Programming, Bioinformatics data analysis (Large-scale (massive) next generation data analysis and critical assessment, relational data bases (my SQL), SNP and microarray data, genomic signal analysis), Applied mathematics, computational modeling and statistics (stochastic simulation, algorithm testing and evaluation, algorithm development and implementation on multiple platforms), as well as Matched experimental and computational protocols for single-cell genomics and transcriptomics.
During the contract period Dr. Vasco made the decision to pursue other carrier opportunities and to leave this position. Please see the activity report during his contract period (link in final periodic report).
Position 1 - replacement/re-recruitment (2nd). Dr. Magda Gaya
After an additional thorough selection procedure to substitute Dr. Vasco, a decision was made to recruit Dr. Magda Gaya. Dr. Gaya holds a PhD in Human Population Genetics from the University of Barcelona and brings along extensive expertise in comparative and functional genomics related to Human polymorphic inversions and Molecular evolution, Biomedical Bioinformatics – Adaptive evolution in the human lineage, and functional analysis of genomes, among other skills.
For details regarding Dr. Gaya’s NewGen project activities during her contract period, please see the final periodic report.
Position 2. A research scientist was hired for the position related to studies on plant adaptation to abiotic stress, in particular, regulation of micronutrient zinc deficiency and tolerance to excess metals in extremophile hyperaccumulator plant species. Following a careful selection process Dr. Ana Gonçalves Leite de Assunção was selected. Dr. Assunção holds a PhD in Ecology and Ecotoxicology of Plants from the Free University of Amsterdam, The Netherlands. She has worked as researcher and project coordinator (NWO-VENI laureate) at the Laboratory of Genetics at Wageningen University, the Netherlands, and at the Department of Plant Biology and Biotechnology at University of Copenhagen, Denmark. She uses physiological, genetic, genomic and molecular biology approaches to study the molecular basis and regulation of micronutrient homeostasis network in the model plant species Arabidopsis as well as in Arabidopsis-related metal hyperaccumulator species. Over the past years Dr. Assunção has built a solid network in this field. For details regarding the project activities during her contract period, please see final periodic report.
Position 3. Following an agreement with the EU Project Officer the initial position of an experienced scientist was changed to an Executive Coordinator position for CIBIO centre. After a careful recruitment process a decision was made to hire Dr. Ana Natália Domingues Dias for this position. Dr. Dias holds a PhD in Marine Ecology from the University of Algarve, and has solid research experience in ecology, biology and evolutionary ecology from a top Environmental Sciences School (School of Environmental Sciences, University of East Anglia, UK) and the University of Valencia. She brought along solid expertise in coordination of large scale international collaboration in research and post-graduation education involving a top world university (MIT) and all the main Portuguese universities; coordination and management of complex administrative tasks; advanced communication skills, namely: communication with a large network of researchers, students and faculty; communication and marketing strategies for managing international recruitment of students and researchers; communication of research and educational achievements to governmental bodies, media and general public; interaction with Portuguese higher education stake holders and main research funding bodies; interaction and communication with companies and other institutions. Project report via link in the final periodic report.
All of the above-indicated researchers have had a great impact on the Next Generation Sequencing related research in their field of Science at CIBIO. Their expertise have specifically strongly enhanced the speed and efficiency with which the Next Generation Sequencing as well as the “Genomics factory” has been implemented.
Twinning: Expertise and know-how exchange, and Training for knowledge transfer to CIBIO
Background
The twinning (Expertise and know-how exchange, and Training for knowledge transfer) in the CIBIO-New-Gen project was divided into two Work packages (WP5 and WP6). WP5 was dedicated to Principal Investigators and/or experienced staff from CIBIO to be engaged in two-sided visits with European and other international research centers of excellence in specific areas of interest, in order to assure a flow of knowledge to CIBIO. The twinning activities had the character of short-term scientific missions, allowing for a regular exchange of scientists from our institution with institutes abroad, aiming to maximize impact and quality of our research. WP6 was primarily devoted to training CIBIO’s more junior or early career researchers, to foster mobility during their education and optimize their gain of knowledge and technological skills from supporting partners and other EU centers of Excellence. This WP was composed by both short and long term training missions. An additional aim was, for both work packages, to strengthen already ongoing partnerships as well as to promote the establishment of new collaborations during the duration of the project and beyond.
The Twinning activities under both WP5 and WP6 did suffer a significant delay as described in the periodic reports. Following the agreed extension of the NewGen project with the EC, the activities have been more effectively planned and the resources extensively explored. Some of the initially planned Twinning activities had to be reprogrammed or even changed to a different twinning partner due to the delay of the project. In total almost 30 training and mobility activities (WP5) have been executed during the project period, involving PI´s and/or experienced staff. Some of these activities had the form of two-sided visits to/from European and other international research centers of excellence in specific areas of interest related to WP5 (for further description see the two periodic reports and in the specific individual deliverable report D6). In other cases where it was not possible to plan in a two-sided twinning within the NewGen project time lines, the CIBIO researcher has performed the visit to the supporting institute, bringing back the much needed know-how to CIBIO for continuous set up and protocol improvement of the installed Next Generation Sequencing platform. In the latter cases a visit from a researcher from the supporting partner institution is planned in and will be supported by other project resources. Eleven junior or early stage career researchers were involved in these Training and mobility activities (WP6), the majority of which being in the form of long term training for effective knowledge transfer to CIBIO which is crucial both when it comes to the implementation of new Next Generation Sequencing approaches/services as well as application of complex downstream data analysis techniques. These Training and Mobility activities that have been executed during the course of the CIBIO-New-Gen project are described in more detail in the specific Deliverable report D8 as well as in the periodic reports.
As indicated above the visits have focused mainly on Next Generation Sequencing techniques implementation, protocol set-up as well as the downstream sequence data analyses methodologies. The exchange and twinning activities also served for an improved integration of CIBIO in the European Research Area, through long lasting partnerships with research groups in Europe and America.
CIBIO-INBIO had a network of research collaborations across Europe and America that was heavily consolidated and expanded through an exchange of know-how and expertise program on several important research areas using Next Generation Sequencing (NGS), through the NEWGEN project, outlined below:
a) Conservation Genetics and Wildlife Management
• Collaboration with Max Planck Institute (Germany) in completing the sequencing of mitochondrial genome of 236 of the sable antelope - Department of Evolutionary Genetics – Advanced DNA Sequencing Techniques.
• Collaboration with the University of Montana (US) regarding analyses of transcriptome sequencing and expression data generated using Next Generation Sequencing technologies in the context of the study of genetic bases of adaptive traits and gene expression - Good Lab – Evolutionary Genomics, Department of Ecosystems and Conservation Sciences.
• Collaboration with Cornell University (US) related to ongoing and future collaborative projects with the main goal of developing a protocol for genomic analysis (Genotyping by Sequencing – GBS) of museum and non-invasive samples - Department of Ecology and Evolutionary Biology.
• Collaboration with the University of São Paulo (Brazil) regarding overall exchange of expertise and limitations using genomics in the field of conservation genetics - Department of Genetics and Evolutionary Biology, Institute of Bioscience (IB).
• Collaboration and cooperation with the University of California Los Angeles (US), on the genome resequencing and analysis of the grey wolf in Europe. This involved both genomics training for the CIBIO-INBIO collaborators as well as development of new pipelines for genomic analysis - Department of Ecology and Evolutionary Biology.
b) Human Evolutionary Genetics
• Collaboration with Max Planck Institute (Germany) in the field of Evolutionary Anthropology.
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c) Tropical Biology
• Collaboration with the Museu Paraense Emílio Goeldi, Federal University of Pará (Brazil), with the focus on implementing a protocol for target capture and massively parallel sequencing of ultra-conserved DNA elements (UCEs) for comparative studies on Neotropical rainforest bird species with shallow evolutionary time scales.
• Joint efforts with Universidade Estadual Paulista (UNESP), Brazil, regarding the development and optimization of a Restriction site Associated DNA sequencing (RADseq) method for three species of Neotropical toads belonging to the Rhinella marina species group.
d) Ecology and Evolution of Aquatic Organisms
• Collaboration with Oxford University focusing on training exchange and discussing future research collaboration and potential application of genome and transcriptome studies to future research lines - Department of Zoology.
• Collaboration with the Romberg Tiburon Center (RTC), California (US) focusing on knowledge transfer, namely on the sequencing of the transcriptome of individuals of the limpet Pattela vulgata.
e) Immunogenetics, Microbes and Infectious Diseases
• Strengthening of existing collaboration with the Swedish Agricultural University, Uppsala (Sweden), regarding metagenomics applications and downstream bioinformatics analysis - Viral Metagenomics and Bioinformatics Group.
• Collaboration with ANSES - French Agency for Food, Environmental, Occupational Health and Safety, Ploufragan (France) focusing on NGS applications in the studies of the rabbit hemorrhagic disease virus (RHDV).
f) Biodiversity of Deserts and Arid Regions
• Collaboration with Virginia Polytechnic Institute and State University (US) and the University of California, Berkeley (US) on the transcriptomics of Salamandra salamandra - Department of Horticulture (Virginia Polytechnic and State University) and the Department of Environmental Science (UC Berkeley).
• Collaboration with the University of Oulu (Finland) focusing on training and collaborative research on genomic signal of ecological diversification and transcriptomic tools applied to behavioral and morphological traits - Department of Biology.
• Collaboration with the University of Jyvaskyla (Finland) in the development of transcriptomic tools for studying behavioral and morphological traits (this collaboration will also be extended to the University of Leipzig).
g) Plant Biology
• Collaboration with the Claude Bernard University, Lyon (France) on genomic characterization of grapevine (Vitis vinifera) cultivars namely, for the identification and comparative evolutionary analysis of specific genes families, such as stilbene synthases, which are important for wine chemical profile and organoleptics - Sex and Evolution Team, Biometrics and Evolutionary Biology Laboratory. This collaboration is paramount to the CIBIO-INBIO’s ongoing research effort to perform genomic characterization of National grapevine varieties, through NGS to resequencing of grapevine genomes.
h) The Applied Ecology
• Collaboration with the Imperial College London (UK) on linking metagenomics and land-use changes. This included the planning for a joint project application regarding this topic in Iberia in a forthcoming call - Forest Ecology and Conservation Research Group.
i) The Applied Phylogenetics – AP group
• Research exchange with the Center for Conservation & Evolutionary Genetics (CCEG), part of the Smithsonian Conservation Biology Institute (SCBI) and based at the National Zoological Park (NZP) of the Smithsonian Institution, US, with the aim to a) develop human resources by means of training in NGS laboratory methods, b) generate genomic datasets for three main research projects in applied phylogenetics, and c) to develop bioinformatics skills by means of a planned workshop at CIBIO-INBIO by researchers of CCEG and SI.
j) Environmental Archaeology and Livestock Genomics and Conservation
• Collaboration with University of California, Davis (US) focusing on knowledge transfer of restriction-site associated DNA sequencing (RADSeq) method, which samples at reduced complexity across target genomes, and promises to deliver high resolution population genomic data - Department of Animal Science.
• Research exchange with Uppsala University (Sweden) to enable CIBIO-INBIO researchers to learn more about the means of collection and analysis of genomic datasets, namely the analysis and assembly of historic cattle and wheat genomes - Ancient DNA laboratory Evolutionary Biology Centre (EBC).
k) The Population Genetics, Hybridization and Speciation
• Collaboration with Uppsala University (Sweden) focusing on several lines of research associated with the mapping of multiple traits of both wild and domestic rabbits. The group in Uppsala is a world-leader in animal genetics and uses both domesticated and natural populations for genetic dissection of simple and complex traits. This collaboration will extend to other animal groups - Functional genomics in domestic animals group (PI: Leif Andersson)
Benefits/Project impact
In addition to what has been outlined above regarding the impact of the CIBIO-New-Gen project, there are additional and extremely important benefits to be reported. Due to CIBIO´s long-standing collaboration and twinning activities, CIBIO was approved to become the first LIA (Laboratoire International Associé) of CNRS (Centre National de la Recherche Scientifique, France) in Portugal. This will be a twinning between CIBIO and Montpellier, France, and is a unique achievement for CIBIO as an institute as well as for Portugal. The EC funded CIBIO-New-Gen project and the implemented NGS platform had profound impact in this CNRS decision. CIBIO has also created the concept of TwinLabs in Portugal, and opened the first one in Angola in October 2012. We are now in the process of negotiating TwinLabs in Morocco, Brazil, and the USA. In great part due to the CIBIO-New-Gen project and the new Genomics Platform, as well as to the well-defined Twinning and Training programs, our PhD Program in Biodiversity, Genetics and Evolution (BIODIV) secured the largest funding given by FCT to any PhD program in the country, all fields. The BIODIV funding is composed by two components: i) the first is a series of 48 PhD scholarships, and ii) the second is a series of 16 PhD scholarships, exclusive for Angolan citizens aiming to develop their research. In total, this corresponds to an amount of 4.5 M€ investment in training awarded to CIBIO. Altogether, this is exactly what would be expected by a CAPACITIES project: capacity building at CIBIO, and is demonstrating that CIBIO is becoming a prestigious international player in its field.
Workshops, conferences, dissemination and visibility
Background
This WP was devoted to the broadening and facilitation of exchange of scientific experience and expertise of CIBIO, as well as to making knowledge available to the general public and the society as a whole.
Updating CIBIO´s website/Implementation of the dedicated CIBIO New-Gen project website
The new CIBIO’s website as well as a CIBIO New-Gen project dedicated website were implemented in the final reporting period. The brand new and extensively improved CIBIO website (http://cibio.up.pt/) was put on-line in September 2014, and a dedicated CIBIO-New-Gen project website (http://cibio-newgen.pt) was soon after linked to this main site. Specific details (and reference to the CIBIO-New-Gen project) were also made available on the CIBIO main website at (http://cibio.up.pt/ctm-molecular-analysis-services) with a link to the specific project website. The CIBIO-New-Gen project website has been continuously updated regarding project activities/news as well as new sequencing services being provided.
Organization of international workshops, national meetings and courses
The international workshops, national meetings and courses organized during the course of the CIBIO-New-Gen project are outlined below. More specific details regarding the meetings were given in the individual Deliverable reports.
1. The Advances in Ecological Speciation (AES) Conference
April 29-30, 2013 | Auditorium - Vairão Campus
The AES conference aims at joining researchers and students from all over the world to present and discuss cutting-edge ecological speciation research. The aim is to provide an informal but stimulating scientific atmosphere, which promote strong interaction and brainstorming between students and more experienced researchers.
The conference included 5 invited plenary talks, 16 oral communications, poster sessions and a round table covering the topics of parallel adaptation, genomics of ecological speciation, adaptive radiations and hybridization, among others.
2. PlantUp - CIBIO Info Meeting
September 16, 2014 | Auditorium - Vairão Campus
This Info Meeting (all in Portuguese) was organized in the context of the CIBIO-New-Gen project and included all the research groups at the University of Porto performing research in plant biology. The meeting consisted of an opening presentation regarding the CIBIO-New-Gen project and the status of the platform installation as well as services provided. This was followed by individual scientific presentations from the respective plant biology groups and concluded with a discussion. Around 60 researchers participated. For the official meeting program, see the individual Deliverable report D11/12.
3. XI CONGRESS OF THE PORTUGUESE ETHOLOGICAL SOCIETY
October 9-10, 2014 | Auditorium - Vairão Campus
CIBIO hosted the 11th Congress of the Portuguese Ethological Society, on the 9th and 10th of October 2014. SPE congresses attract most researchers and students working on animal behaviour in Portugal, and are an opportunity to meet leading international invited speakers. The congress covers all research areas in animal behaviour, and talks are given in English. This congress highlights the emerging area of behavioural genetics, with two invited speakers from this area: Nadia Aubin-Horth (Université Laval, Québec) and Adam Jones (Texas A&M University). Invited speaker Marta Moita (Champalimaud Neuroscience Programme, Lisbon) will talk about neuroscience of fear, and László Garamszegi (Estación Biológica de Doñana, Seville) about phylogenetic meta-analyses of behaviour.
4. TiBE 2015 – Global Biodiversity Change – from Genes to Ecosystems
1st and 2nd June 2015 | Auditorium - Vairão Campus
The TiBE 2015 conference provided a broad perspective on recent advances in the study of the ecological impacts of social and economic drivers, land-use dynamics, biological invasions, species range and niche dynamics, genetic structure and flow, and other dimensions of change in ecosystems, landscapes and their biodiversity. Furthermore the conference allowed a direct link with applied ecology including: i) the detection, interpretation and forecast of changes in a given territory; ii) the anticipation of trends in the patterns of drivers of ecological change, and the early detection of biodiversity responses and ecosystem changes; and iii) the support to model-assisted frameworks for cost-efficient conservation and monitoring. The program included four scientific sessions, each with a plenary conference by an invited international expert and several communications proposed by the conference participants.
5. GENOMICS SEMINAR/WORKSHOP
June 18-19, 2015 | Auditorium - Vairão Campus
A 2–day Genomics Seminar/Workshop was organized in the context of the CIBIO-New-Gen project, and being part of a complete Genomics Week at the institute (see also under organized courses/workshops below). During these two days, five major topics in genomics research in the area of Next Generation Sequencing were covered:
1. Environmental Genomics;
2. Phylogenomics;
3. Conservation/Population Genomics;
4. AgriGenomics;
5. One Health Genomics.
6. Next Generation Sequencing Info Afternoon @ CIBIO-InBIO
September 30, 2015 | Auditorium - Vairão Campus
This Next Generation Sequencing (NGS) information afternoon included presentations from CIBIO researchers as well as by researchers from other Portuguese research centers, and covered the following NGS application projects: The Cork Oak sequencing project, AgriGenomics, Using NGS to understand genome reticulation and adaptive phenotypes challenged by climate change, Conservation and evolutionary genomics of the shad species, Alosa alosa (Savél) and A. fallax (Savelha) in Portugal and throughout Eurasia, and Marine Genomics. This was also the official conclusion of the CIBIO New-Gen project as well as the kick-off session for the ERA Chair in Environmental Metagenomics, EnvMetaGen – Horizon 2020 –WIDESPREAD awarded to CIBIO in 2015. A number of companies, representatives from the University of Porto, FCT (the Portuguese national funding agency for science, research and technology), as well as representatives and researchers from other research institutes attended the event. There were around 80 participants in total. The official meeting program is presented on the individual Deliverable report D11/12.
In addition to the above described workshops and meetings, a number of courses were also organized in the scope of the CIBIO-New-Gen project. These courses are outlined below and described in more detail in the Deliverable report D11/12:
1. WORKSHOP GENOTYPING-BY-SEQUENCING (GBS): USES AND ABUSES May 30, 2014 | Vairão Campus
Genotyping-by-Sequencing (GBS) is potentially a very useful technique for genotyping model and non-model organisms quickly and cheaply at many thousands of loci simultaneously. However, the technique is relatively new and specific considerations and biases are starting to emerge. In this workshop, Thomas White (Cornell University, USA and Canterbury Christ Church University, UK) described how to conduct a GBS analysis, from tissue collection to bioinformatics analysis. Tom highlighted some of the potential pitfalls on the way, and possible solutions.
2. WORKSHOP 'INTRODUCTION TO RAD DATA ANALYSIS September 24-26, 2014 | Vairão Campus
This was a three-day course by Dr. Alan Brelsford, Univ. Lausanne, which covered the following topics:
1. Introduction to Unix command-line environment
2. De-multiplexing and quality control of raw sequence data
3. Analysis of GBS/RAD data without a reference genome using Stacks
4. Analysis of GBS/RAD data with a reference genome using Bowtie/Samtools
5. Export and quality filtering of raw genotypes using Vcftools
3. ADVANCED COURSE GENOTYPING BY SEQUENCING (GBS): PRINCIPLES, APPROACHES AND APPLICATIONS June 15-17, 2015 | Vairão Campus
This aim of the course was to give attendees a broad overview of Genotyping-by-Sequencing (GBS), including the principles of how data are obtained by the various different approaches, and their advantages and disadvantages. A question and answer session helped to determine the right approach for different study systems or special cases, such as degraded DNA. There were also practical data-analysis sessions, where attendees were guided through example data processing with various analysis tools.
4. INTRODUCTION TO NEXT-GENERATION SEQUENCING DATA AND ANALYSIS COURSE
June 23-26, 2015 | Vairão Campus
This course provided an introduction to the basics of next generation sequencing data and analysis, and includes hands-on exercises throughout.
Topics covered include:
1. Basics of the Linux command line;
2. DNA/RNA preparation and sequencing technologies, including reduced-representation sequencing;
3. What to do with newly-delivered sequencing data;
4. Assembling sequences of varying sizes and complexities;
5. Variant discovery;
6. Annotation of small to large datasets;
7. Ancient and variable-coverage DNA;
8. Transcriptomes and gene expression analysis; and
9. Walkthroughs of example analyses.
Emphasis throughout was on understanding fundamentals, and on developing skills for design of practical sequencing projects and analysis of sequencing data in light of research questions and biological and practical limitations.
TV documentaries
The production of the series of 13 TV-documentaries on biodiversity has been concluded and resulted in a unique project of science dissemination. Negotiations have so far been concluded with the Portuguese first TV channel RTP1. The series of documentaries will be broadcasted on prime time, substituting a high profile BBC Nature series. Each documentary is briefly outlined below:
1. Crocodiles in the deserts of Mauritania
A group of biologists investigates the biology of crocodiles isolated in mountain oases of the Sahara, in Mauritania. The genetic analysis of collected samples allows the analysis of population connectivity and differentiation. The episode describes the work of senior biologist José Carlos Brito and twining with different Universities in Spain, Morocco and Mauritania.
2. The expansion of cashew plantations in Guinea-Bissau
In the last decades the plantations of cashew have been expanding considerably in Guinea-Bissau, substituting the native forest or rice, the basic food of people. This episode follows the impact of cashew plantations in biodiversity, economy and Guinean society, through the research work of Luís Catarino, and twinning with local institutions and the Tropical Biology Institute (IICT).
3. Investigating cooperative breeding in birds in South Africa
Social weavers live in large communities and build huge nests in the trees of southern Kalahari, South Africa. Research in cooperative breeding in birds analyses the behaviour of social weavers, in particular seeking to understand the role of helpers during the breeding season. This episode follows the work of biologist Rita Covas, and twinning with local institutions, and the Universities of Montpellier (France) and Sheffield (UK).
4. Using tree-frogs to understand the evolution of the Atlantic Forest (Brasil)
The movements of a group of species with low vagility can help to understand the evolution of the habitats in which they occur. In this episode, the study of tree-frogs included in the genus Phyllomedusa is exemplified in order to reconstruct the evolution of the Brasilian Atlantic Forest. This is the work of biologist Fernando Sequeira, and twinning with the Universities of São Paulo (USP), Federal do Pará (UFP) and Estadual de São Paulo (UNESP), all in Brazil.
5. Portugal: an European hotspot of bat diversity
Bats represent about 25% of mammals in the planet. This episode relates how research has been increasing knowledge on the more than 20 species occurring in Portugal, and helping conservation programs. This work is headed by biologist Hugo Rebelo, and includes the development of new capture techniques as well as twinning with the University of Bristol (UK) and the Doñana Biological Station (Seville, Spain).
6. Distribution and characterization of the reptiles from Cape Verde
The genetic analyses of reptile species in all islands of the Cape Verde archipelago allowed the correction of old classification mistakes and suggested new distribution maps. This knowledge is of crucial relevance for the conservation and reserve planning in the country. This episode follows the research of Raquel Vasconcelos and twinning with local institutions.
7. São Tomé e Príncipe: the highest rate of bird endemism in the world
When a population of a species is split in two and the groups are no longer in contact, they generally follow different and divergent evolutionary trajectories, adapting to different habitats. This project aims to understand this process using the birds of São Tomé e Príncipe (Gulf of Guinea, Africa) as a model system. This episode follows the work of biologist Martim Melo, and twinning with local and South-African institutions.
8. Conservation of migratory fish species in Europe
Migratory anadromous fish feed and grow in the sea, but spawn in freshwater. Due to the construction of dams in most European rivers, some populations were able to adapt to freshwater and exhibit a sedentary lifecycle. This episode follows the research of Paulo Alexandrino and seeks to understand the evolutionary and genetic mechanisms which allowed this process. Twinning with different institutions in France and Italy is described.
9. Conservation genetics of intriguing sloth species in Brasil and Panama
Sloths live in the tropical forests of Central and South America. Recent deforestation in the Amazon and Atlantic Forest is a serious threat to this group of unique species. Using genetic tools, researchers aim to understand the consequences of forest fragmentation on the conservation programs of sloths. This episode follows the work of biologist Nadia Moraes-Barros and twinning with Brazilian and European institutions.
10. Understanding human admixture in the Cape Verde islands
Using one of the most admixed human populations in the planet, it was possible to better understand the genetic mechanisms which are responsible for eye and skin pigmentation. In addition, genetic data allowed the reconstruction of the colonization history of the archipelago. This episode describes the work of biologist Jorge Rocha, and twinning with the Universities of Cabo Verde, Stanford (USA), and the Max-Planck Institute (Leipzig, Germany).
11. Following the steps of terrible invader: the cane toad
A group of Portuguese and Brazilian researchers is reconstructing the evolutionary and adaptation history of the cane toad, starting in its native distribution area, the Amazon, to the recent and uncontrolled invasion of the Australian territory. This episode follows the research of biologist Fernando Sequeira and twinning with both Brasilian (Universidade Federal do Pará) and Australian Universities (Universities of Townsville and Melbourne).
12. Recovery and conservation of the Purple Gallinule in the Mediterranean
The purple gallinule is an iconic bird from the Mediterranean. While in the Roman period it was considered as an ornamental bird and depicted in mosaics all over the Mediterranean, in more recent times was almost driven to extinction due to human persecution. This episode follows the work of Ricardo Lopes who, using molecular and ecological tools, has inspired reintroductions and conservation programs in different European countries.
13. Understanding the history of domestication
Domestication of animals and plants changed completely the history of human societies, and is also the major experiment ever made in biology. Rabbits are the only species domesticated in Western Europe, and offer a unique model to better understand the molecular bases underlying domestication. This episode follows the research of Nuno Ferrand and melts genomics with French medieval history, from monasteries to modern Museums.
Publication of booklets
Two booklets disseminating the information about the current Next Generation Sequencing project activities at CIBIO have been produced. The titles of the two booklets are indicated below:
1. Next Generation Sequencing projects at CIBIO-InBIO – Conservation and Metagenomics
2. Next Generation Sequencing projects at CIBIO-InBIO – Evolution
(ISBN - ISBN - 978-989-99518-0-8)
Participation of CIBIO´s researchers in high-level international conferences
Seventeen participations by CIBIO researchers at 10 different high-level international conferences have taken place during this final periodic reporting period. The list of conference participations is outlined in the individual Deliverable report D13. The 10 different high-level conferences attended are listed below:
1. Cordon Research Conference in Speciation 2015, Ventura, USA
2. Botany 2015, Edmonton, Alberta, Canada
3. The Viral Hepatitis Congress 2015, Kap Europa, Frankfurt, Germany
4. SMBE 2015 –Society for Molecular Biology and Evolution, Vienna, Austria
5. 6th International Barcode of Life Conference 2015, Guelph, Canada
6. ESEB 2015 | European society for evolutionary biology 2015, Lausanne, Switzerland
7. 6th Congress of European Microbiologists (FEMS 2015), Maastricht, The Netherlands
8. The 2nd Microbe R&D and Business Collaboration Forum Europe, London,
9. Evolution 2015, Guarujá, Brazil
10. 7th European Congress of Mammalogy, Stockholm University, Sweden
Organization of Seminars including FP7 encouragement topic and establishment of consortia
The seminars organized within the context of the CIBIO-New-Gen project under the course of the project are outlined below. These seminars were disseminated widely and were open for researchers from other scientific institutes, companies with interest in the scientific field as well as the general public:
1. John Archer, CIBIO-InBIO/UP - Involved in the establishment of a Bioinformatics unit at CIBIO SLAYING THE CHIMERA IN VENOM GLAND TRANSCRIPTOMICS - January 21, 2015
2. Antonio Muñoz, CIBIO-InBIO/UP – Involved in the establishment of a Bioinformatics unit at CIBIO RETROSPECTIVE OF MY WORK IN BIOINFORMATICS: SQUEEZING DATA TO GET INFORMATION - January 30, 2015
3. Lee Ann Rollins, Deakin University, Australia - INVASIVE SPECIES AS A MODEL FOR THE STUDY OF RAPID EVOLUTION - July 20, 2015
4. Tomas Larsson, University of Gothenburg, Sweden - DE NOVO SEQUENCING OF “UNCONVENTIONAL” SPECIES - PROMISES, PROGRESS AND PITFALLS - June 29, 2015
5. Courtney Hofman, Center for Conservation and Evolutionary Genetics, Smithsonian Institution & University of Oklahoma's Laboratories of Molecular Anthropology and Microbiome Research, USA - ARCHAEOGENOMICS IN THE ANTHROPOCENE - September 28, 2015
6. Love Dalén, Swedish Museum of Natural History, Sweden - USING ANCIENT GENOMES TO EXAMINE POPULATION DEMOGRAPHY, DIVERGENCE AND GENETIC STOCHASTICITY - September 21, 2015
In the context of the impact and benefits of the NewGen project, InBIO/CIBIO has become a partner of a recently approved FCT Research Infrastructure, GenomePortugal, as well as the leading/coordinating Institution for a second approved FCT Research Infrastructure, PORBIOTA.
GenomePortugal is a distributed genome sequencing and analysis RI for basic/applied genome research and advanced services. Its main objectives are: i) potentiate the participation of Portuguese scientists in national and international genome projects and ii) develop clinical, environmental, marine and agrofood genomics, biotechnology and green chemistry. GenomePortugal congregates the national research centers involved in genomic research, brings over 3 million euros of investment in DNA sequencing and analysis instruments, over 40 researchers and technical personnel, and important bioinformatics expertise dispersed across a wide geographical area, under the umbrella of a professionally managed RI.
PORBIOTA is a research infrastructure, which aims to collect, store and manage all kinds of biodiversity data from the entire Portuguese territory. It will be connected to LIFEWATCH, which is its European counterpart. PORBIOTA will promote a national agenda on biodiversity survey and research, providing services to the administration, the scientific community, and society. The consortium includes top national research centres, natural history museums, the Portuguese node of GBIF, the LTER Portugal network, ICOS Portugal, the Azorean Biodiversity Portal, and the Nature Conservation and Forests institute (ICNF). The direct impact and connection from the CIBIO-New-Gen project to/and from PORBIOTA is through the powerful data analysis platform implemented in the New-Gen project (additional data processing and storage power will be purchased through the PORBIOTA project to upgrade the existing platform).
In connection to this WP7 task a project application (Project entitled “EnvMetaGen – Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics”) was submitted by CIBIO within the scope the European Commission call Horizon 2020-WIDESPREAD-2104-2, extensively utilizing the NGS platform implemented during the CIBIO-New-Gen project. The project was approved and was initiated in September this year, with a kick off meeting organized jointly with the concluding meeting of the New-Gen project (September 30, 2015).
Society/Industry/SMEs info days and impact
A number of combined scientific and Next Generation Sequencing platform information days, open to researchers, companies and the public in general, have been organized as also outlined above: i) An info day for researchers and groups at the University of Porto performing research in the area of plant biology. The meeting consisted of an opening presentation regarding the CIBIO-New-Gen project and the status of the platform installation as well as services provided. This was followed by individual scientific presentations from the respective plant biology groups; ii) A two-day Genomics Seminar/Workshop, being part of a complete Genomics week at the institute. The two days involved seminars with both a research approach and commercial touch (in the areas of Environmental Genomics, Phylogenomics, Conservation/Population Genomics, AgriGenomics and One Health Genomics) and were open to scientists, companies and the general public; and iii) a Next Generation Sequencing Info Afternoon (also serving as the conclusive meeting for the CIBIO-New-Gen project), involving a closing/status presentation regarding the CIBIO-New-gen project, but also specific presentations regarding Next Generation Sequencing applications of ongoing projects. The meeting was open for the general public, researchers and companies. A number of companies and institutions/organizations were invited and among those present were representatives from EDP (a leading company in the energy sector in Portugal), Stab-Vida (a Portuguese biotech/genetics company), University of Porto (represented by the Vice-Dean, Maria João Ramos), FCT (the Portuguese national funding agency for science, research and technology), INIAV (State Laboratory related to the Agricultural Research and Veterinarian Science), and CCMAR (Research Centre from the University of Algarve).
The impact of the above mentioned meetings (as well as the additionally organized meetings and seminars indicated further above) was great. We have had a number of service requests/collaboration proposals from other research institutes, governmental organizations (e.g. the Portuguese National Institute for Health), and a number of hospitals. Some of these activities are already ongoing and others are currently being planned.
In addition, we continue our collaboration with StabVida regarding commercialization of services related to genetics and are in negotiations regarding collaborations on Next Generation Sequencing service provision.
CIBIO is presently concluding discussions with a French Biotech company, ANTAGENE, that is interested in opening a company (a subsidiary or more likely a separate company with strong connections to ANTAGENE) together with CIBIO (collaboration regarding NGS services). ANTAGENE is a biotechnology company specialized in providing services in the area of DNA analysis (domestic and wild animals) and the idea is to expand this service portfolio using the broad expertise CIBIO has, developments made by the institute’s researchers, and the implemented NGS and data analysis platform (CIBIO-New-Gen project). In this first phase the plan is to establish the new company in Portugal and the rest of the Iberian Peninsula in the areas of: a) Bovine Selection, b) Wildlife genetics (in both Europe and Africa), c) Environmental DNA (e.g. Fresh water quality, soil quality/component etc), as well as d) Current ANTAGENE services in DNA testing for certification of origin and disease prevention. The new company will initially be based at the CIBIO facilities at the University of Porto campus in Vairão. The intention and aim is to employ personnel holding a PhD for positions in the areas of commercialization, implementation of novel DNA tests, scientific management within the company, as well as for the applied research and development.
CIBIO has furthermore ongoing collaboration protocols and support with/from EDP – “Energias de Portugal, S.A.” in the area of biodiversity and is also coordinating a REN Chair in Biodiversity (co-sponsored by REN – National Energy Networks and FCT - the Portuguese national funding agency for science, research and technology).
CIBIO-New-Gen project Impact and Benefits
Further to the CIBIO-New-Gen project impact described above it should also be mentioned that in the last couple of years, the project coordinator has been responsible for the building of a project to fully recover the old Museum of Natural History and Science of the University of Porto. We were successful in getting a grant from Structural Funds through the Northern Region of Portugal of over 4.5 M€ to prepare the new Hall of Biodiversity in one of the most iconic and symbolic houses of Porto, the Andresen House. Financial support was also provided from the Vice-Dean of the University of Porto. This is paving the way for winning the organization of ECSITE 2017 in Porto, joining more than 1300 people from all over the world working in Scientific Museums and Centres. Benefiting from this situation, dissemination of science for the general public will be a joint activity involving both CIBIO and the Natural History and Science Museum of the University of Porto.
Potential Impact:
The CIBIO-New-Gen project allowed CIBIO to strengthen significantly its research profile and potential, raising its capacity to establish collaborations both at national and international levels. The acquisition of the most powerful next generation genome sequencer in Portugal and the extensive interchange program for students and researchers allowed the institute to upgrade its research and computing infrastructure and to train its staff in new cutting edge methodologies used in the emerging area of genomics. All of this turned the institute much more attractive for researchers and research institutions. This capacity is most relevant not only for attracting new talent and collaborations but also for retaining talent, reversing brain drain, and developing into higher levels existing collaborations. Through the CIBIO-New-Gen project, CIBIO became a stronger player both in the Portuguese research system and in the European Research Area. Below we will give more detail on various impacts of the project.
Better integration of CIBIO in the European Research Area, through long lasting partnerships with research groups in Europe and America
CIBIO has a network of research collaborations across Europe and America that was consolidated and expanded through an exchange of know-how and expertise program on several important research areas using Next Generation Sequencing (NGS), through the CIBIO-New-Gen project.
a) Conservation Genetics and Wildlife Management
• Collaboration with Max Planck Institute (Germany) in completing the sequencing of mitochondrial genome of 236 of the sable antelope - Department of Evolutionary Genetics – Advanced DNA Sequencing Techniques.
• Collaboration with the University of Montana (US) regarding analyses of transcriptome sequencing and expression data generated using Next Generation Sequencing technologies in the context of the study of genetic bases of adaptive traits and gene expression - Good Lab – Evolutionary Genomics, Department of Ecosystems and Conservation Sciences.
• Collaboration with Cornell University (US) related to ongoing and future collaborative projects with the main goal of developing a protocol for genomic analysis (Genotyping by Sequencing – GBS) of museum and non-invasive samples - Department of Ecology and Evolutionary Biology.
• Collaboration with the University of São Paulo (Brazil) regarding overall exchange of expertise and limitations using genomics in the field of conservation genetics - Department of Genetics and Evolutionary Biology, Institute of Bioscience (IB).
• Collaboration and cooperation with the University of California Los Angeles (US), on the genome resequencing and analysis of the grey wolf in Europe. This involved both genomics training for the CIBIO-INBIO collaborators as well as development of new pipelines for genomic analysis - Department of Ecology and Evolutionary Biology.
b) Human Evolutionary Genetics
• Collaboration with Max Planck Institute (Germany) in the field of Evolutionary Anthropology.
c) Tropical Biology
• Collaboration with the Museu Paraense Emílio Goeldi, Federal University of Pará (Brazil), with the focus on implementing a protocol for target capture and massively parallel sequencing of ultra-conserved DNA elements (UCEs) for comparative studies on Neotropical rainforest bird species with shallow evolutionary time scales.
• Joint efforts with Universidade Estadual Paulista (UNESP), Brazil, regarding the development and optimization of a Restriction site Associated DNA sequencing (RADseq) method for three species of Neotropical toads belonging to the Rhinella marina species group.
d) Ecology and Evolution of Aquatic Organisms
• Collaboration with Oxford University focusing on training exchange and discussing future research collaboration and potential application of genome and transcriptome studies to future research lines - Department of Zoology.
• Collaboration with the Romberg Tiburon Center (RTC), California (US) focusing on knowledge transfer, namely on the sequencing of the transcriptome of individuals of the limpet Pattela vulgata.
e) Immunogenetics, Microbes and Infectious Diseases
• Strengthening of existing collaboration with the Swedish Agricultural University, Uppsala (Sweden), regarding metagenomics applications and downstream bioinformatics analysis - Viral Metagenomics and Bioinformatics Group.
• Collaboration with ANSES - French Agency for Food, Environmental, Occupational Health and Safety, Ploufragan (France) focusing on NGS applications in the studies of the rabbit hemorrhagic disease virus (RHDV).
f) Biodiversity of Deserts and Arid Regions
• Collaboration with Virginia Polytechnic Institute and State University (US) and the University of California, Berkeley (US) on the transcriptomics of Salamandra salamandra - Department of Horticulture (Virginia Polytechnic and State University) and the Department of Environmental Science (UC Berkeley).
• Collaboration with the University of Oulu (Finland) focusing on training and collaborative research on genomic signal of ecological diversification and transcriptomic tools applied to behavioral and morphological traits - Department of Biology.
• Collaboration with the University of Jyvaskyla (Finland) in the development of transcriptomic tools for studying behavioral and morphological traits (this collaboration will also be extended to the University of Leipzig).
g) Plant Biology
• Collaboration with the Claude Bernard University, Lyon (France) on genomic characterization of grapevine (Vitis vinifera) cultivars namely, for the identification and comparative evolutionary analysis of specific genes families, such as stilbene synthases, which are important for wine chemical profile and organoleptics - Sex and Evolution Team, Biometrics and Evolutionary Biology Laboratory. This collaboration is paramount to the CIBIO-INBIO’s ongoing research effort to perform genomic characterization of National grapevine varieties, through NGS to resequencing of grapevine genomes.
h) The Applied Ecology
• Collaboration with the Imperial College London (UK) on linking metagenomics and land-use changes. This included the planning for a joint project application regarding this topic in Iberia in a forthcoming call - Forest Ecology and Conservation Research Group.
i) The Applied Phylogenetics – AP group
• Research exchange with the Center for Conservation & Evolutionary Genetics (CCEG), part of the Smithsonian Conservation Biology Institute (SCBI) and based at the National Zoological Park (NZP) of the Smithsonian Institution, US, with the aim to a) develop human resources by means of training in NGS laboratory methods, b) generate genomic datasets for three main research projects in applied phylogenetics, and c) to develop bioinformatics skills by means of a planned workshop at CIBIO-INBIO by researchers of CCEG and SI.
j) Environmental Archaeology and Livestock Genomics and Conservation
• Collaboration with University of California, Davis (US) focusing on knowledge transfer of restriction-site associated DNA sequencing (RADSeq) method, which samples at reduced complexity across target genomes, and promises to deliver high resolution population genomic data - Department of Animal Science.
• Research exchange with Uppsala University (Sweden) to enable CIBIO-INBIO researchers to learn more about the means of collection and analysis of genomic datasets, namely the analysis and assembly of historic cattle and wheat genomes - Ancient DNA laboratory Evolutionary Biology Centre (EBC).
k) The Population Genetics, Hybridization and Speciation
• Collaboration with Uppsala University (Sweden) focusing on several lines of research associated with the mapping of multiple traits of both wild and domestic rabbits. The group in Uppsala is a world-leader in animal genetics and uses both domesticated and natural populations for genetic dissection of simple and complex traits. This collaboration will extend to other animal groups - Functional genomics in domestic animals group (PI: Leif Andersson)
Upgrading the RTD capacity and capability of CIBIO as well as the quality of research carried out by CIBIO.
A large part of our research lines requires DNA level analysis of biological diversity. During the last years new technologies arose, and now the trend is to look at whole genomes or part of genomes: the genomics era has arrived. To be able to accompany the fast development of this new and important area and develop state of the art research and education we had the necessity to acquire additional research capacity for analysis, which was possible through the NEWGEN Project. With this project we could buy the most advanced next-generation sequencing platform in the country, recruit experienced researchers and train our staff and students in the new techniques to produce and handle NGS data. Genome sequencing generates an extraordinary amount of data, which require highly specialized professionals, larger computing capacity, namely storage and analytical capacity for downstream sequence analysis and for modelling approaches. All of this we could achieve with the NEWGEN project. In addition to purchasing the NGS platform, we upgraded our computing capacity and we created a new research team of bioinformaticians who have been giving a huge support to the other researchers in the institute in moving to the new era of genomics. As an example, in the last national call for research grants of FCT (National Foundation for Science and Technology), all the 82 research proposals submitted by our researchers involved NGS methods and the bioinformatics researchers were part of the research teams of all the projects. As a result, we had a success rate of 23% compared to a national average success rate of 13%.
Improved research capacity for increased contribution to regional economic and social development
Before the CIBIO-New-Gen project, Portugal as a whole, and the North convergence region in particular, did not possess a core next-gen sequencing facility and the associated bioinformatics for conducting state of the art genomics analysis. With the implementation of CIBIO-next-gen, we were able to provide these resources and give the region and the country the opportunity to integrate these new technologies into the research and education systems.
We increased the capacity of CIBIO to provide services to regional and national authorities, companies and other research centres and we are presently able to provide a number of specific NGS services, which is an important asset for the sustainability of the Centre and also to the socio-economic development of the North region. Becoming a highly specialized scientific and technological service provider, raised the prestige and technological profile of the institute and of the region. The number of NGS services clients is steadily increasing, currently including the National Health Institute (INSA) and a number of national research centres and institutes.
In addition, the CIBIO-New-Gen project helped CIBIO to attract and retain excellent professionals, allowing us to counteract the brain drain which has been affecting severely the North region and Portugal as whole, over the last years, due to the economic crisis. This centre has increased the number of researchers with a PhD during the CIBIO-NewGen project: in 2011 the centre had 137 researchers with a PhD and in 2015 it has 164.
Research infrastructure establishment
The technological capacitation by CIBIO-New-Gen was paramount for CIBIO to be an important player on the recently created Portuguese Roadmap for Research Infrastructures. In this context CIBIO is currently leading the Portuguese E-Infrastructure for Information and Research on Biodiversity – PORBIOTA, and is an active member of two other infrastructures: National Facility for Genome Sequencing and Analysis – GenomePortugal, and Portuguese Research Infrastructure of Scientific Collections – PRISC.
The purpose of the PORBIOTA infrastructure is to collect and manage biodiversity data from across the country and promote a national agenda of monitoring and research in biodiversity and provide services to the scientific community, policy makers, managers and the general public. PORBIOTA hopes to contribute to increase public awareness of the importance of biodiversity and improve scientific culture through science programs for citizens and other popular science programs. The infrastructure is managed by a consortium that includes top national research units, with significant experience in research in biodiversity and in the development of computer-supported technologies, natural history museums, the Portuguese node of GBIF (Global Biodiversity Information Facility), and the National Authority for Nature and Forest Conservation (ICNF). The infrastructure will be integrated into LIFEWATCH (ESFRI), the European e-infrastructure for research on biodiversity and ecosystems.
GenomePortugal is a distributed infrastructure for genome sequencing. Its main objectives are: i) to enhance the participation of Portuguese scientists in national and international projects in genomics and, ii) to develop clinical genomics, environmental, marine and food processing, biotechnology and environmental chemistry. GenomePortugal brings together national research centers involved in genome sequencing spread across a wide geographical area and is expected to put Portugal on the map of countries with technological capacity and experience to sequence complex genomes and to involve our scientific community in the genomics revolution currently underway. The main lines of action of this distributed infrastructure are: a) to develop a cadre of very specialized staff to operate installed instruments and to analyze data and simultaneously, improving computational power and bioinformatics tools; b) to provide high standards of training in NGS analysis, through the organization of Summer Schools and Workshops, microarray and bioinformatics methodologies, open to national and international students and researchers; and c) sequencing genomes of scientific and economic relevance to Portugal. This infrastructure is of strategic relevance because genome sequencing and analysis is fueling a major revolution in the biological, biomedical, environmental, agrofood and marine sciences, with visible impact on biotechnology, green chemistry, management of natural resources and health. By building the research capacity and aligning its research strategy with the Regional, National and European development priorities for the 2015-2020 period, GenomePortugal will make measurable contributions to regional development, the national economy and to retain highly qualified human resource.
PRISC is a research infrastructure focusing on the conservation, study and accessibility of Portuguese scientific collections. PRISC will provide the present and future Portuguese scientific collections high standards of preservation conditions, inventory and accessibility to allow them to be increasingly used for scientific research, postgraduate education and the promotion of scientific culture in Portugal, and will support directly the development of research and innovation in all areas of sciences and humanities through increased use of Portuguese scientific collections.
Involvement in regional Authorities and Private entities
CIBIO is deeply involved with regional authorities and private companies in the assessment, minimization and compensation of the environmental impacts of large infrastructure development, such as road infrastructures, railway lines, power distribution networks, and dams. CIBIO-INBIO’s activity thus contributes for the sustainable regional development, by providing solutions, which blend the needs of social and economic development with that of environmental protection. This includes the scientific analysis of environmental impacts and technical design of compensatory mitigation frameworks, as well as the development of scientifically sound monitoring programs. This work is carried out by two autonomous units in the institute: Centre for Molecular Analysis (CTM) and Centre for Studies and Projects in Applied Ecology (GEPE). While CTM is dedicated to applied research on the evaluation and use of animal and plant genetic resources, GEPE provides services in biodiversity conservation and monitoring. Both units work on technology transfer and develop partnerships with private national and foreign companies and governmental bodies. In addition, we have a program of Invited Research Chairs co-funded by FCT and large industry partners: a) EDP Biodiversity Chair (power production and distribution systems); b) Infrastructures of Portugal Biodiversity Chair (roads and railway lines); and c) REN in Biodiversity Chair (energy transmission systems).
CIBIO provides many services and customized research for industry. Currently we have contracts with 22 different companies. We were asked by a biotechnology French company, Antagen, to create a Portuguese branch for them, Antagene Portugal.
The improvement of our research capacities has increased our contributions to the sustainable regional development, by fostering the application of novel knowledge and techniques to the practical solution of critical environmental problems. This includes, for instance, the increasing use of genetic tools in impact assessment, non-invasive monitoring of animal populations, and analysis of difficult to study population processes such as dispersal, among other applications.
Improvement of participation of CIBIO in FP7 projects and H2020
During the CIBIO-New-Gen project the participation of CIBIO in European research projects has increased compared to previous years. This was translated into five grants from FP7 and four from H2020 framework programs. These projects have brought 3.6 M € to the institute.
Particularly, we would like to highlight the ERA Chair granted in early 2015. The Era Chair application ‘Capacity Building at CIBIO for Research and Innovation Using Environmental Metagenomics’ (Acronym: EnvMetaGen) was based on the increased research capacity in gene sequencing CIBIO acquired through the CIBIO-New-Gen project and was funded by the EU with 2,4 M€. The project aims to expand the research and innovation potential of CIBIO through the creation of an ERA Chair in Environmental Metagenomics. The goal is to strengthen the research potential of human resources, lab facilities and next-generation genome sequencing equipment, supporting an emerging research line in environmental metagenomics for applications in biodiversity conservation, invasive species control, ecosystem services assessment, and environmental (bio)monitoring. The EnvMetaGen is allowing us to launch an international tender for hiring a top researcher as well as her/his team in order to promote adequate critical mass in the area of environmental metagenomics. It is expected that this area of research will have an impact both at regional, national and European level, creating innovative and low cost approaches and methodologies for the study of biodiversity, ecology and environmental quality.
Furthemore, CIBIO has been developing other important research collaborations with international partners. In 2014 we created the International Associated Laboratory (LIA) ‘Biodiversity and Evolution’ with a focus on biodiversity and evolutionary biology. The LIA established a formal cooperation between the Centre National de la Recherche Scientifique (CNRS), the Université Montpellier 2 Sciences et Techniques (UM2), the Institut de Recherche pour le Développement (IRD), the École Pratique Hautes Études (EPHE), France, and CIBIO-INBIO, the University of Porto and the Portuguese Science and Technology Foundation (FCT), built upon several well established collaborations between CIBIO and the French research units. In 2013 our researcher Rui Figueira created, and leads since then, the Portuguese Node of GBIF (Global Biodiversity Information Facility). CIBIO-INBIO is the leader of the research e-infrastructure ‘PORBIOTA’, created in 2015, which will collect, store and manage all biodiversity data from the Portuguese territory and will be connected to its European counterpart LIFEWATCH. PORBIOTA includes, among other members, LTER Portugal, the Portuguese node of LTER (Long-Term Ecological Research Network of sites where long term ecological investigation is carried out) and ICOS Portugal, the Portuguese node of ICOS (Pan-European research infrastructure for Integrated Carbon Observation System). We are also formal members of the EUBON project (Building the European Biodiversity Observation Network) and participate in several collaborative research networks funded by COST Actions.
Sustainability of the measures beyond the project lifetime
CIBIO has several contracts with enterprises and other public and private entities in the areas of ecological inventory and monitoring, biodiversity management and conservation with special interest for game management, environmental impact assessment and natural resources valorization. Excellence in research and renovated capacity, as well as the new bioinformatics capacity allowed us to seek for more sustainability measures and new sponsors to our research. For instance, this year we have made a research contract with REN (major company of energy transmission systems) and FCT, for a 3 years research chair which funds the salary and research of a senior researcher (total of 480.000€). Also this year we negotiated the extension of the research chair with Infrastructures of Portugal (large road and railway company) for two additional years (160.000€). This chair supports the salary of a senior researcher and three post-docs.
CIBIO is presently concluding discussions with the French Biotech company ANTAGENE, about opening a company (a subsidiary or more likely a separate company with strong connections to ANTAGENE). ANTAGENE is a biotechnology company specialized in providing services in the area of DNA analysis (domestic and wild animals) and they wish to expand this service portfolio using the broad expertise of CIBIO in this field, namely recent technical developments made by our researchers, which involve the NGS and data analysis platform (NewGen). In this first phase the plan is to establish the new company in Portugal to reach the rest of the Iberian Peninsula in the areas of: a) bovine delection, b) wildlife genetics (in both Europe and Africa), c) environmental DNA (e.g. fresh water quality, soil quality/component etc), and d) current ANTAGENE services in DNA testing for certification of origin and disease prevention. The new company will initially be based at CIBIO facilities. We plan to employ personnel with a PhD degree for the areas of commercialization, implementation of novel DNA tests, scientific management, and applied research and development.
During 2015 we have also signed several contracts for assessing and following up environmental impacts in the construction of important human-made structures at national level, such as windmill farms, dams and linear structures (roads and rail trains). This work includes the proposal of minimization and compensation measures, inventory and characterization of fauna, including vertebrates and invertebrates, flora and habitats of terrestrial, freshwater and coastal ecosystems, monitoring programs for endangered plant and animal populations located in areas affected by human-made structures and development and validation of new methodologies used in wildlife management and ecological monitoring.
Commercialization of services provided by CIBIO´s Centre for Molecular Analysis (CTM) together with the ongoing collaboration with the Biotech/Genetics company StabVida provide an important and regular income for the centre.
Dissemination of knowledge and spreading of excellence
The improvement of public appreciation and understanding of biodiversity and evolutionary biology is a priority mission of CIBIO. Our researchers are actively committed into a diversified range of science dissemination and outreach initiatives.
During the CIBIO-New-Gen project the following activities were performed:
A large numbers of international workshops, national meetings and courses have been organized during the course of the CIBIO-New-Gen project and in the context of science dissemination and outreach initiatives: The Advances in Ecological Speciation (AES) Conference (April, 2013), PlantUp – CIBIO Next Generation Sequencing Info Meeting (September, 2014), the XI Congress Of The Portuguese Ethological Society (October, 2014), the TiBE 2015 – Global Biodiversity Change – from Genes to Ecosystems conference (June, 2015), the Genomics Seminar/Workshop (June, 2015), Next Generation Sequencing Info Afternoon @ CIBIO-InBIO, (September, 2015), and the Next Generation Sequencing workshops/courses: Workshop Genotyping-By-Sequencing (GBS): Uses And Abuses (May, 2014), Workshop 'Introduction To Rad Data Analysis (September 24-26, 2014), Advanced Course Genotyping By Sequencing (GBS): Principles, Approaches And Applications (June 15-17, 2015), Introduction To Next-Generation Sequencing Data And Analysis Course (June 23-26, 2015).
TV documentaries
A production of a number of TV-documentaries on biodiversity has been concluded and has resulted in a unique project of science dissemination. Negotiations have so far been concluded with the Portuguese first TV channel RTP1. The series of documentaries will be broadcasted on prime time.
Publication of booklets
For further develop its current activities, CIBIO will strengthen meetings with science journalists, to promote communication links and attain successful science dissemination. Along these lines 2 booklets have been produced regarding, i) Next Generation Sequencing Projects at CIBIO-INBIO – Conservation and Metagenomics, and ii) Next Generation Sequencing Projects at CIBIO-INBIO – Evolution
Society and Industry info days and establishment of partnerships
A number of combined scientific and Next Generation Sequencing platform information days, open to researchers, companies and the public in general, have been organized as also outlined above: i) An info day for researchers and groups at the University of Porto performing research in the area of plant biology. The meeting consisted of an opening presentation regarding the CIBIO-New-Gen project and the status of the platform installation as well as services provided. This was followed by individual scientific presentations from the respective plant biology groups; ii) A two-day Genomics Seminar/Workshop, being part of a complete Genomics week at the institute. The two days involved seminars with both a research approach and commercial touch (in the areas of Environmental Genomics, Phylogenomics, Conservation/Population Genomics, AgriGenomics and One Health Genomics) and were open to scientists, companies and the general public; and iii) a Next Generation Sequencing Info Afternoon (also serving as the conclusive meeting for the CIBIO-New-Gen project), involving a closing/status presentation regarding the CIBIO-New-gen project, but also specific presentations regarding Next Generation Sequencing applications of ongoing projects. The meeting was open for the general public, researcher and companies. A number of companies and institutions/organizations were invited and among those present were representatives from EDP (a leading company in the energy sector in Portugal), Stab-Vida (a Portuguese biotech/genetics company), University of Porto, FCT (the Portuguese national funding agency for science, research and technology), INIAV (State Laboratory related to the Agricultural Research and Veterinarian Science), and CCMAR (from the University of Algarve). These activities in combination with the extensive Twinning and know-how transfer/exchange activities outlined above have strengthened ongoing collaborations and paved the way for new partnerships.
After the conclusion of the CIBIO-New-Gen project, we anticipate that the many hired researchers will continue to strengthen CIBIO’s research excellence, since major efforts for sustainability will most surely lead to a growth environment and expansion.
It should be stated in the end here that the dissemination will continue through courses, conference organization as well as conference participation and scientific publications (important to note is that many more publications are in the pipeline and will come out after the conclusion of the project – delay of project and the set-up of the platform to produce data for publication caused this delay).
List of Websites:
http://cibio-newgen.pt/homepage
http://cibio.up.pt/
Prof. Nuno Ferrand ICETA - Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Porto, Portugal
Tel.: +351252660411
Email: cibio.up@cibio.up.pt