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Promoting SINgle cell GEnomics to explore the ecology and evolution of hidden microeuKaryotes

Periodic Reporting for period 1 - SINGEK (Promoting SINgle cell GEnomics to explore the ecology and evolution of hidden microeuKaryotes)

Reporting period: 2016-01-01 to 2017-12-31

Most of the extant diversity of eukaryotes remains poorly characterized, limiting society's understanding of, for example, the rise and diversification of parasite lineages, the evolutionary origin and variability of metabolic and cellular networks, and which microbes provide which functions in the global environment. However, classical methodologies have provided limited progress in our understanding of eukaryotic biology. Single cell genomics (SCG) is one of the most promising modern techniques, given its capacity to provide genomic information of one cell at a time, a possibility unimaginable only 10 years ago. Applying SCG to microbial eukaryotes is still in its infancy, and is particularly challenging when compared to SCG on prokaryotes, because of target genomes of greater complexity. However, the exploitation of SCG in this field is crucial for two main reasons:
1. De novo genomes from uncultured lineages
2. Genome variability within a microbial population

There are obviously challenges and practical barriers to explore SCG to its full potential and the main objective of the SINGEK ITN project is therefore to train a new generation of researchers in SCG of microbial eukaryotes and do so by addressing a set of fundamental and inter-related scientific questions. SCG on microbial eukaryotes requires interdisciplinary interactions, justifying the dedicated and synergistic effort proposed in this project. Our team of 15 ESRs is being involved in all steps in the process encompassing complementary technological and scientific backgrounds (laboratory, bioinformatics, ecology and evolution). The ESR integration in the planned research is being accomplished by collegiate scientific direction, training events and courses of transferable skills, and secondments to basic and applied research institutes and private enterprises.
The SINGEK ITN project has overall progressed according to plan in this period from 01/01/2016 (M1) and 31/12/2017 (M24), leading to the following achievements:

Kick-off Meeting, Meeting Recruitment Committee, Opening Meeting including ESRs, 1st BCN ITN Science Slam, SINGEK Supervisory Board (SSB) Meeting, Mid-Term Meeting.

Workshop on Collaborative learning, core communication skills and time/project management, Workshop on Genomics, Workshop on Communicating Science Online, Workshop on Research Ethics, Workshop on Single Cell Sorting and Analysis, Workshop on Genome Assembly and Workshop on Advanced Scientific Writing.

Logo & brand identity, Website ( Intranet Site, Facebook page, Research Gate profile, Twitter account (@SINGEK_ITN), Introductory video ( Internal forum tool, Blog and project (

Kick-off meeting, Consortium Agreement, A web page established, ESRs recruited, Facebook established, PCDPs accepted, Introductory video (instead of initial conceived exhibition), A procedure for single cell sorting and genome sequencing, A procedure for genome bioinformatic analysis and Mid-term review and adjustment.
The core of the research programme of the SINGEK ITN project covers all aspects of the SCG pipeline: (WP3) Laboratory work, from single cells to sequences, (WP4) Bioinformatics, (WP5) Application of SCG in microbial ecology and (WP6) Application of SCG in microbial evolution. The scientific activities and major research questions addressed up to now by all ESRs are:

ESR4: Javier Florenza (PI: S. Bertilsson) - WP3
Improving SCG by applying to several interesting cases

ESR12: Jari Iannucci (PI: S. Pagliara) - WP3
Use of microfluidics to sort, grow and study interactions in individual algal cells

ESR6: Atafeh Lafzi (PI: I. Gut / H. Heyn) - WP4
Single cell transcriptome profiles: from sequences to biological facts. Part in two non-microbial projects

ESR10: François Bucchini (PI: K. Vandepoele) - WP4
New tools for genome annotation in unknown microeukaryote lineages

ESR15: Imer Muhovic (PI: A. Mascarell) - WP4
Development of a web-based software to facilitate SCG analysis

ESR1: Aurelie Labarre (PI: R. Massana / T. Richards) - WP5
Comparative genomics of stramenopiles to infer ecological lifestyles. Phagocytosis focus

ESR2: Ina Deutschmann (PI: R. Logares) - WP5
Improving network analysis tools to investigate interactions within microbial communities

ESR8: Laura Rubinat (PI: C. de Vargas) - WP5
Environmental (biodiversity and functional genomics) study of marine mixotrophy

ESR11: Vanessa Smilanski (PI: T. Richards) - WP5
Study of the infection (morbid versus chronic) of parasitic perkinsid against tadpoles

ESR14: Alexandra Beliavskaia (PI: A. Darby) - WP5
Biodiversity of eukaryote microbes associated with blood-feeding arthropods

ESR3: Konstantina Mitsi (PI: I. Ruiz-Trillo) - WP6
Increase taxon sampling to improve the opisthokont tree and find the genome profile of animal's ancestor

ESR5: Max Emil Schön (PI: T. Ettema) - WP6
Study the origin of the eukaryotic cell, through phylogenomics(tree of life) and the role of endosymbiosis

ESR7: Luis Javier Galindo (PI: P. López-García) - WP6
Improve the deep eukaryotic phylogeny by single cell phylogenomics

ESR9: Luis Felipe de Almeida Benites (PI: G. Piganeau) - WP6
Genome evolution within mamiellophytes, with emphasis on sexual imprints (Big Outlier Chromosome)

ESR13: Raphael Gollnisch (PI: K. Rengefors / D. Ahrén) - WP6
Population genetics (by SCG) of an invasive harmful algae: genomic variation and dispersal patterns

The SINGEK Consortium envisages a number of aspects which will have a long-term impact on the ESRs’ career prospects: (1) a cross disciplinary environment, (2) a dedicated scientific training programme, (3) an extensive training and mentoring programme on complementary skills, (4) a primary tool to facilitate the progress of their individual research (Personal Career Development Plan) and (5) secondments. In overall, being part of the SINGEK Consortium is enhancing ESR’s knowledge and skills beyond what would be possible by individual organisations.

For the SINGEK host institutions, their ability to attract high qualified and talented ESRs has provided a significant impact. The visibility of the activities undertaken by all SINGEK Consortium Members is being increased with the involvement of ESRs, which are playing a key role in the establishment of new interactions and collaborations.

As a benefit for the European Research Area, the SINGEK Consortium was conceived to bring together individual partners from different sectors with varied and diverse expertises under one umbrella to cover all aspects of an emerging technology with high scientific potential: Single Cell Genomics (SCG). So, for the first time a complementary group of scientists is now working together to develop this science providing the opportunity for the European research environment to take a lead in this emerging field for the coming years. The networking of SINGEK scientific teams and their associat