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

Informazioni relative al progetto

SINGEK

ID dell’accordo di sovvenzione: 675752

DOI

10.3030/675752

Progetto chiuso

Data della firma CE 20 Luglio 2015

Data di avvio 1 Gennaio 2016

Data di completamento 31 Maggio 2020

Finanziato da

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Costo totale

€ 3 889 393,20

Contributo UE

€ 3 889 393,20

Coordinato da

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Other (19)

Presentation of results in international scientific conferences
An optimized procedure for SAG/T sequencing
A refined eukaryotic tree of life
Reconstruction of functional and metabolic pathways of several eukaryotes
Identification of key genes or gene families related to ecological performance
Inventories of microeukaryotic diversity in contrasted ecosystems, including novelty

Inventories of microeukaryotic diversity in contrasted ecosystems, including novelty

Scientific Conference: European SCG Meeting
A SAG database repository with tools for downloading and gene searching
Evolution of gene repertoire across the tree of life through comparative genomics
Global distribution of species and functions by comparing SAGs to major metagenomes
Disentangling deep evolutionary events (plastid endosymbiosis, origins of multicellularity)
Pipelines for de novo assembly of Illumina data into contigs depending on the sample
An optimized procedure for library preparation for sequencing SAG/SATs
Models of microeukaryote population genetics and genomics

Models of microeukaryote population genetics and genomics

An optimized procedure for single cell sorting
Pipelines for gene detection and annotation of novel taxa
A procedure to check the quality of the initial reads and the large assemblies
Scientific papers published in international high-profile peer-reviewed journals
An optimized procedure for genome or transcriptome amplification from single cells

Websites, patent fillings, videos etc. (3)

The SINGEK Web page
Popularizations events
Report of the main interactions between microeukaryotes and other organisms

Report of the main interactions between microeukaryotes and other organisms

Pubblicazioni

Peer reviewed articles (25)

Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells

Autori: Jean-François Mangot, Ramiro Logares, Pablo Sánchez, Fran Latorre, Yoann Seeleuthner, Samuel Mondy, Michael E. Sieracki, Olivier Jaillon, Patrick Wincker, Colomban de Vargas, Ramon Massana
Pubblicato in: Scientific Reports, Numero 7, 2017, Pagina/e 41498, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/srep41498

Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes

Autori: L. Felipe Benites, Nicole Poulton, Karine Labadie, Michael E. Sieracki, Nigel Grimsley, Gwenael Piganeau
Pubblicato in: Philosophical Transactions of the Royal Society B: Biological Sciences, Numero 374/1786, 2019, Pagina/e 20190089, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2019.0089

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems

Autori: M. E. Sieracki, N. J. Poulton, O. Jaillon, P. Wincker, C. de Vargas, L. Rubinat-Ripoll, R. Stepanauskas, R. Logares, R. Massana
Pubblicato in: Scientific Reports, Numero 9/1, 2019, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-019-42487-1

Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium

Autori: Luis Javier Galindo, Guifré Torruella, David Moreira, Hélène Timpano, Gita Paskerova, Alexey Smirnov, Elena Nassonova, Purificación López-García
Pubblicato in: Genome Biology and Evolution, Numero 10/10, 2018, Pagina/e 2736-2748, ISSN 1759-6653
Editore: Oxford University Press
DOI: 10.1093/gbe/evy205

PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics

Autori: Schön, Max E.; Eme, Laura; Ettema, Thijs J.G.
Pubblicato in: Bioinformatics, Numero 36(6), 2019, Pagina/e 1718–1724, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1101/688465

Single cell ecology

Autori: Thomas A. Richards, Ramon Massana, Stefano Pagliara, Neil Hall
Pubblicato in: Philosophical Transactions of the Royal Society B: Biological Sciences, Numero 374/1786, 2019, Pagina/e 20190076, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2019.0076

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

Autori: Andrea Del Cortona, Christopher J. Jackson, François Bucchini, Michiel Van Bel, Sofie D’hondt, Pavel Škaloud, Charles F. Delwiche, Andrew H. Knoll, John A. Raven, Heroen Verbruggen, Klaas Vandepoele, Olivier De Clerck, Frederik Leliaert
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 117/5, 2020, Pagina/e 2551-2559, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.1910060117

Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

Autori: Guy Leonard, Aurélie Labarre, David S. Milner, Adam Monier, Darren Soanes, Jeremy G. Wideman, Finlay Maguire, Sam Stevens, Divya Sain, Xavier Grau-Bové, Arnau Sebé-Pedrós, Jason E. Stajich, Konrad Paszkiewicz, Matthew W. Brown, Neil Hall, Bill Wickstead, Thomas A. Richards
Pubblicato in: Open Biology, Numero 8/1, 2018, Pagina/e 170184, ISSN 2046-2441
Editore: Royal Society Publishing
DOI: 10.1098/rsob.170184

Genome Resolved Biogeography of Mamiellales

Autori: Jade Leconte, L. Felipe Benites, Thomas Vannier, Patrick Wincker, Gwenael Piganeau, Olivier Jaillon
Pubblicato in: Genes, Numero 11/1, 2020, Pagina/e 66, ISSN 2073-4425
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes11010066

Disentangling the mechanisms shaping the surface ocean microbiota

Autori: Ramiro Logares; Ina M. Deutschmann; Pedro C. Junger; Caterina R. Giner; Anders K. Krabberød; Thomas S.B. Schmidt; Laura Rubinat-Ripoll; Mireia Mestre; Guillem Salazar; Clara Ruiz-González; Marta Sebastián; Colomban de Vargas; Silvia G. Acinas; Carlos M. Duarte; Josep M. Gasol; Ramon Massana
Pubblicato in: Microbiome, 2020, ISSN 2049-2618
Editore: BioMed Central Ltd.
DOI: 10.21203/rs.2.17228/v2

Identity Noise and Adipogenic Traits Characterize Dermal Fibroblast Aging

Autori: Marion Claudia Salzer, Atefeh Lafzi, Antoni Berenguer-Llergo, Catrin Youssif, Andrés Castellanos, Guiomar Solanas, Francisca Oliveira Peixoto, Camille Stephan-Otto Attolini, Neus Prats, Mònica Aguilera, Juan Martín-Caballero, Holger Heyn, Salvador Aznar Benitah
Pubblicato in: Cell, Numero 175/6, 2018, Pagina/e 1575-1590.e22, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2018.10.012

Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates

Autori: Aurelie Labarre, Aleix Obiol, Susanne Wilken, Irene Forn, Ramon Massana
Pubblicato in: Limnology and Oceanography, Numero 65/S1, 2020, ISSN 0024-3590
Editore: American Society of Limnonogy and Oceanography
DOI: 10.1002/lno.11379

Diverse alveolate infections of tadpoles, a new threat to frogs?

Autori: Aurelie Chambouvet, Vanessa Smilansky, Miloslav Jirků, Marcos Isidoro-Ayza, Sarah Itoïz, Evelyne Derelle, Adam Monier, David J. Gower, Mark Wilkinson, Michael J. Yabsley, Julius Lukeš, Thomas A. Richards
Pubblicato in: PLOS Pathogens, Numero 16/2, 2020, Pagina/e e1008107, ISSN 1553-7374
Editore: Public Library of Science
DOI: 10.1371/journal.ppat.1008107

Virus-host coexistence in phytoplankton through the genomic lens

Autori: Sheree Yau, Marc Krasovec, L. Felipe Benites, Stephane Rombauts, Mathieu Groussin, Emmelien Vancaester, Jean-Marc Aury, Evelyne Derelle, Yves Desdevises, Marie-Line Escande, Nigel Grimsley, Julie Guy, Hervé Moreau, Sophie Sanchez-Brosseau, Yves van de Peer, Klaas Vandepoele, Sebastien Gourbiere, Gwenael Piganeau
Pubblicato in: Science Advances, Numero 6/14, 2020, Pagina/e eaay2587, ISSN 2375-2548
Editore: American Association for the Advancement of Science
DOI: 10.1126/sciadv.aay2587

Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies

Autori: Atefeh Lafzi, Catia Moutinho, Simone Picelli, Holger Heyn
Pubblicato in: Nature Protocols, Numero 13/12, 2018, Pagina/e 2742-2757, ISSN 1754-2189
Editore: Nature Publishing Group
DOI: 10.1038/s41596-018-0073-y

A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades

Autori: Konstantina Mitsi, Alicia S. Arroyo, Iñaki Ruiz-Trillo
Pubblicato in: Biology Letters, Numero 15/9, 2019, Pagina/e 20190182, ISSN 1744-9561
Editore: The Royal Society
DOI: 10.1098/rsbl.2019.0182

Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics

Autori: Yaiza M. Castillo, Jean‐François Mangot, Luiz Felipe Benites, Ramiro Logares, Megumi Kuronishi, Hiroyuki Ogata, Olivier Jaillon, Ramon Massana, Marta Sebastián, Dolors Vaqué
Pubblicato in: Molecular Ecology, Numero 28/18, 2019, Pagina/e 4272-4289, ISSN 0962-1083
Editore: Blackwell Publishing Inc.
DOI: 10.1111/mec.15210

Linking metagenomics to aquatic microbial ecology and biogeochemical cycles

Autori: Hans‐Peter Grossart, Ramon Massana, Katherine D. McMahon, David A. Walsh
Pubblicato in: Limnology and Oceanography, Numero 65/S1, 2020, ISSN 0024-3590
Editore: American Society of Limnonogy and Oceanography
DOI: 10.1002/lno.11382

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

Autori: Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J. McCarthy, Adrián Álvarez-Varela, Eduard Batlle, Sagar, Dominic Grün, Julia K. Lau, Stéphane C. Boutet, Chad Sanada, Aik Ooi, Robert C. Jones, Kelly Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Caroline Braeuning, Cornelius Fischer, Sascha Sauer, Timo Trefzer, Christian Con
Pubblicato in: Nature Biotechnology, Numero 38/6, 2020, Pagina/e 747-755, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1038/s41587-020-0469-4

Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage

Autori: Naoji Yubuki, Luis Javier Galindo, Guillaume Reboul, Purificación López-García, Matthew W Brown, Nicolas Pollet, David Moreira
Pubblicato in: Molecular Biology and Evolution, Numero 37/3, 2019, Pagina/e 651-659, ISSN 0737-4038
Editore: Oxford University Press
DOI: 10.1093/molbev/msz250

Uncovering microbial inter-domain interactions in complex communities

Autori: Javier Florenza, Manu Tamminen, Stefan Bertilsson
Pubblicato in: Philosophical Transactions of the Royal Society B: Biological Sciences, Numero 374/1786, 2019, Pagina/e 20190087, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2019.0087

Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi

Autori: Luis Javier Galindo, Guifré Torruella, David Moreira, Yana Eglit, Alastair G. B. Simpson, Eckhard Völcker, Steffen Clauß, Purificación López-García
Pubblicato in: Philosophical Transactions of the Royal Society B: Biological Sciences, Numero 374/1786, 2019, Pagina/e 20190094, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2019.0094

Gene space completeness in complex plant genomes

Autori: Michiel Van Bel, François Bucchini, Klaas Vandepoele
Pubblicato in: Current Opinion in Plant Biology, Numero 48, 2019, Pagina/e 9-17, ISSN 1369-5266
Editore: Elsevier BV
DOI: 10.1016/j.pbi.2019.01.001

Genome Analyses of the Microalga Picochlorum Provide Insights into the Evolution of Thermotolerance in the Green Lineage

Autori: Marc Krasovec, Emmelien Vancaester, Stephane Rombauts, François Bucchini, Sheree Yau, Claire Hemon, Hugo Lebredonchel, Nigel Grimsley, Hervé Moreau, Sophie Sanchez-Brosseau, Klaas Vandepoele, Gwenael Piganeau
Pubblicato in: Genome Biology and Evolution, Numero 10/9, 2018, Pagina/e 2347-2365, ISSN 1759-6653
Editore: Oxford University Press
DOI: 10.1093/gbe/evy167

Ciliate diversity and distribution across horizontal and vertical scales in the open ocean

Autori: Oriol Canals, Aleix Obiol, Imer Muhovic, Dolors Vaqué, Ramon Massana
Pubblicato in: Molecular Ecology, Numero 29/15, 2020, Pagina/e 2824-2839, ISSN 0962-1083
Editore: Blackwell Publishing Inc.
DOI: 10.1111/mec.15528