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

Información del proyecto

SINGEK

Identificador del acuerdo de subvención: 675752

DOI

10.3030/675752

Proyecto cerrado

Fecha de la firma de la CE 20 Julio 2015

Fecha de inicio 1 Enero 2016

Fecha de finalización 31 Mayo 2020

Financiado con arreglo a

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Coste total

€ 3 889 393,20

Aportación de la UE

€ 3 889 393,20

Coordinado por

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

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

Publicaciones

Peer reviewed articles (25)

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

Autores: 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
Publicado en: Scientific Reports, Edición 7, 2017, Página(s) 41498, ISSN 2045-2322
Editor: 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

Autores: L. Felipe Benites, Nicole Poulton, Karine Labadie, Michael E. Sieracki, Nigel Grimsley, Gwenael Piganeau
Publicado en: Philosophical Transactions of the Royal Society B: Biological Sciences, Edición 374/1786, 2019, Página(s) 20190089, ISSN 0962-8436
Editor: 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

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

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

Autores: Luis Javier Galindo, Guifré Torruella, David Moreira, Hélène Timpano, Gita Paskerova, Alexey Smirnov, Elena Nassonova, Purificación López-García
Publicado en: Genome Biology and Evolution, Edición 10/10, 2018, Página(s) 2736-2748, ISSN 1759-6653
Editor: Oxford University Press
DOI: 10.1093/gbe/evy205

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

Autores: Schön, Max E.; Eme, Laura; Ettema, Thijs J.G.
Publicado en: Bioinformatics, Edición 36(6), 2019, Página(s) 1718–1724, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1101/688465

Single cell ecology

Autores: Thomas A. Richards, Ramon Massana, Stefano Pagliara, Neil Hall
Publicado en: Philosophical Transactions of the Royal Society B: Biological Sciences, Edición 374/1786, 2019, Página(s) 20190076, ISSN 0962-8436
Editor: Royal Society of London
DOI: 10.1098/rstb.2019.0076

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 117/5, 2020, Página(s) 2551-2559, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.1910060117

Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

Autores: 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
Publicado en: Open Biology, Edición 8/1, 2018, Página(s) 170184, ISSN 2046-2441
Editor: Royal Society Publishing
DOI: 10.1098/rsob.170184

Genome Resolved Biogeography of Mamiellales

Autores: Jade Leconte, L. Felipe Benites, Thomas Vannier, Patrick Wincker, Gwenael Piganeau, Olivier Jaillon
Publicado en: Genes, Edición 11/1, 2020, Página(s) 66, ISSN 2073-4425
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes11010066

Disentangling the mechanisms shaping the surface ocean microbiota

Autores: 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
Publicado en: Microbiome, 2020, ISSN 2049-2618
Editor: BioMed Central Ltd.
DOI: 10.21203/rs.2.17228/v2

Identity Noise and Adipogenic Traits Characterize Dermal Fibroblast Aging

Autores: 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
Publicado en: Cell, Edición 175/6, 2018, Página(s) 1575-1590.e22, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1016/j.cell.2018.10.012

Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates

Autores: Aurelie Labarre, Aleix Obiol, Susanne Wilken, Irene Forn, Ramon Massana
Publicado en: Limnology and Oceanography, Edición 65/S1, 2020, ISSN 0024-3590
Editor: American Society of Limnonogy and Oceanography
DOI: 10.1002/lno.11379

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

Autores: 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
Publicado en: PLOS Pathogens, Edición 16/2, 2020, Página(s) e1008107, ISSN 1553-7374
Editor: Public Library of Science
DOI: 10.1371/journal.ppat.1008107

Virus-host coexistence in phytoplankton through the genomic lens

Autores: 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
Publicado en: Science Advances, Edición 6/14, 2020, Página(s) eaay2587, ISSN 2375-2548
Editor: American Association for the Advancement of Science
DOI: 10.1126/sciadv.aay2587

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

Autores: Atefeh Lafzi, Catia Moutinho, Simone Picelli, Holger Heyn
Publicado en: Nature Protocols, Edición 13/12, 2018, Página(s) 2742-2757, ISSN 1754-2189
Editor: 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

Autores: Konstantina Mitsi, Alicia S. Arroyo, Iñaki Ruiz-Trillo
Publicado en: Biology Letters, Edición 15/9, 2019, Página(s) 20190182, ISSN 1744-9561
Editor: The Royal Society
DOI: 10.1098/rsbl.2019.0182

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

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

Linking metagenomics to aquatic microbial ecology and biogeochemical cycles

Autores: Hans‐Peter Grossart, Ramon Massana, Katherine D. McMahon, David A. Walsh
Publicado en: Limnology and Oceanography, Edición 65/S1, 2020, ISSN 0024-3590
Editor: American Society of Limnonogy and Oceanography
DOI: 10.1002/lno.11382

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

Autores: 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
Publicado en: Nature Biotechnology, Edición 38/6, 2020, Página(s) 747-755, ISSN 1087-0156
Editor: Nature Publishing Group
DOI: 10.1038/s41587-020-0469-4

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

Autores: Naoji Yubuki, Luis Javier Galindo, Guillaume Reboul, Purificación López-García, Matthew W Brown, Nicolas Pollet, David Moreira
Publicado en: Molecular Biology and Evolution, Edición 37/3, 2019, Página(s) 651-659, ISSN 0737-4038
Editor: Oxford University Press
DOI: 10.1093/molbev/msz250

Uncovering microbial inter-domain interactions in complex communities

Autores: Javier Florenza, Manu Tamminen, Stefan Bertilsson
Publicado en: Philosophical Transactions of the Royal Society B: Biological Sciences, Edición 374/1786, 2019, Página(s) 20190087, ISSN 0962-8436
Editor: 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

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

Gene space completeness in complex plant genomes

Autores: Michiel Van Bel, François Bucchini, Klaas Vandepoele
Publicado en: Current Opinion in Plant Biology, Edición 48, 2019, Página(s) 9-17, ISSN 1369-5266
Editor: 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

Autores: 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
Publicado en: Genome Biology and Evolution, Edición 10/9, 2018, Página(s) 2347-2365, ISSN 1759-6653
Editor: Oxford University Press
DOI: 10.1093/gbe/evy167

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

Autores: Oriol Canals, Aleix Obiol, Imer Muhovic, Dolors Vaqué, Ramon Massana
Publicado en: Molecular Ecology, Edición 29/15, 2020, Página(s) 2824-2839, ISSN 0962-1083
Editor: Blackwell Publishing Inc.
DOI: 10.1111/mec.15528