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

Project Information

SINGEK

Grant agreement ID: 675752

DOI

10.3030/675752

Project closed

EC signature date 20 July 2015

Start date 1 January 2016

End date 31 May 2020

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 3 889 393,20

EU contribution

€ 3 889 393,20

Coordinated by

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

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

Publications

Peer reviewed articles (25)

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

Author(s): 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
Published in: Scientific Reports, Issue 7, 2017, Page(s) 41498, ISSN 2045-2322
Publisher: 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

Author(s): L. Felipe Benites, Nicole Poulton, Karine Labadie, Michael E. Sieracki, Nigel Grimsley, Gwenael Piganeau
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 374/1786, 2019, Page(s) 20190089, ISSN 0962-8436
Publisher: 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

Author(s): M. E. Sieracki, N. J. Poulton, O. Jaillon, P. Wincker, C. de Vargas, L. Rubinat-Ripoll, R. Stepanauskas, R. Logares, R. Massana
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-42487-1

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

Author(s): Luis Javier Galindo, Guifré Torruella, David Moreira, Hélène Timpano, Gita Paskerova, Alexey Smirnov, Elena Nassonova, Purificación López-García
Published in: Genome Biology and Evolution, Issue 10/10, 2018, Page(s) 2736-2748, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evy205

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

Author(s): Schön, Max E.; Eme, Laura; Ettema, Thijs J.G.
Published in: Bioinformatics, Issue 36(6), 2019, Page(s) 1718–1724, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1101/688465

Single cell ecology

Author(s): Thomas A. Richards, Ramon Massana, Stefano Pagliara, Neil Hall
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 374/1786, 2019, Page(s) 20190076, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2019.0076

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

Author(s): 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
Published in: Proceedings of the National Academy of Sciences, Issue 117/5, 2020, Page(s) 2551-2559, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1910060117

Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

Author(s): 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
Published in: Open Biology, Issue 8/1, 2018, Page(s) 170184, ISSN 2046-2441
Publisher: Royal Society Publishing
DOI: 10.1098/rsob.170184

Genome Resolved Biogeography of Mamiellales

Author(s): Jade Leconte, L. Felipe Benites, Thomas Vannier, Patrick Wincker, Gwenael Piganeau, Olivier Jaillon
Published in: Genes, Issue 11/1, 2020, Page(s) 66, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes11010066

Disentangling the mechanisms shaping the surface ocean microbiota

Author(s): 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
Published in: Microbiome, 2020, ISSN 2049-2618
Publisher: BioMed Central Ltd.
DOI: 10.21203/rs.2.17228/v2

Identity Noise and Adipogenic Traits Characterize Dermal Fibroblast Aging

Author(s): 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
Published in: Cell, Issue 175/6, 2018, Page(s) 1575-1590.e22, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2018.10.012

Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates

Author(s): Aurelie Labarre, Aleix Obiol, Susanne Wilken, Irene Forn, Ramon Massana
Published in: Limnology and Oceanography, Issue 65/S1, 2020, ISSN 0024-3590
Publisher: American Society of Limnonogy and Oceanography
DOI: 10.1002/lno.11379

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

Author(s): 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
Published in: PLOS Pathogens, Issue 16/2, 2020, Page(s) e1008107, ISSN 1553-7374
Publisher: Public Library of Science
DOI: 10.1371/journal.ppat.1008107

Virus-host coexistence in phytoplankton through the genomic lens

Author(s): 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
Published in: Science Advances, Issue 6/14, 2020, Page(s) eaay2587, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.aay2587

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

Author(s): Atefeh Lafzi, Catia Moutinho, Simone Picelli, Holger Heyn
Published in: Nature Protocols, Issue 13/12, 2018, Page(s) 2742-2757, ISSN 1754-2189
Publisher: 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

Author(s): Konstantina Mitsi, Alicia S. Arroyo, Iñaki Ruiz-Trillo
Published in: Biology Letters, Issue 15/9, 2019, Page(s) 20190182, ISSN 1744-9561
Publisher: The Royal Society
DOI: 10.1098/rsbl.2019.0182

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

Author(s): Yaiza M. Castillo, Jean‐François Mangot, Luiz Felipe Benites, Ramiro Logares, Megumi Kuronishi, Hiroyuki Ogata, Olivier Jaillon, Ramon Massana, Marta Sebastián, Dolors Vaqué
Published in: Molecular Ecology, Issue 28/18, 2019, Page(s) 4272-4289, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.15210

Linking metagenomics to aquatic microbial ecology and biogeochemical cycles

Author(s): Hans‐Peter Grossart, Ramon Massana, Katherine D. McMahon, David A. Walsh
Published in: Limnology and Oceanography, Issue 65/S1, 2020, ISSN 0024-3590
Publisher: American Society of Limnonogy and Oceanography
DOI: 10.1002/lno.11382

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

Author(s): 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
Published in: Nature Biotechnology, Issue 38/6, 2020, Page(s) 747-755, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-020-0469-4

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

Author(s): Naoji Yubuki, Luis Javier Galindo, Guillaume Reboul, Purificación López-García, Matthew W Brown, Nicolas Pollet, David Moreira
Published in: Molecular Biology and Evolution, Issue 37/3, 2019, Page(s) 651-659, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msz250

Uncovering microbial inter-domain interactions in complex communities

Author(s): Javier Florenza, Manu Tamminen, Stefan Bertilsson
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 374/1786, 2019, Page(s) 20190087, ISSN 0962-8436
Publisher: 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

Author(s): Luis Javier Galindo, Guifré Torruella, David Moreira, Yana Eglit, Alastair G. B. Simpson, Eckhard Völcker, Steffen Clauß, Purificación López-García
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 374/1786, 2019, Page(s) 20190094, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2019.0094

Gene space completeness in complex plant genomes

Author(s): Michiel Van Bel, François Bucchini, Klaas Vandepoele
Published in: Current Opinion in Plant Biology, Issue 48, 2019, Page(s) 9-17, ISSN 1369-5266
Publisher: 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

Author(s): 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
Published in: Genome Biology and Evolution, Issue 10/9, 2018, Page(s) 2347-2365, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evy167

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

Author(s): Oriol Canals, Aleix Obiol, Imer Muhovic, Dolors Vaqué, Ramon Massana
Published in: Molecular Ecology, Issue 29/15, 2020, Page(s) 2824-2839, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.15528