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

Informacje na temat projektu

SINGEK

Identyfikator umowy o grant: 675752

DOI

10.3030/675752

Projekt został zamknięty

Data podpisania przez KE 20 Lipca 2015

Data rozpoczęcia 1 Stycznia 2016

Data zakończenia 31 Maja 2020

Finansowanie w ramach

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Koszt całkowity

€ 3 889 393,20

Wkład UE

€ 3 889 393,20

Koordynowany przez

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

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

Publikacje

Peer reviewed articles (25)

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

Autorzy: 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
Opublikowane w: Scientific Reports, Numer 7, 2017, Strona(/y) 41498, ISSN 2045-2322
Wydawca: 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

Autorzy: L. Felipe Benites, Nicole Poulton, Karine Labadie, Michael E. Sieracki, Nigel Grimsley, Gwenael Piganeau
Opublikowane w: Philosophical Transactions of the Royal Society B: Biological Sciences, Numer 374/1786, 2019, Strona(/y) 20190089, ISSN 0962-8436
Wydawca: 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

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

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

Autorzy: Luis Javier Galindo, Guifré Torruella, David Moreira, Hélène Timpano, Gita Paskerova, Alexey Smirnov, Elena Nassonova, Purificación López-García
Opublikowane w: Genome Biology and Evolution, Numer 10/10, 2018, Strona(/y) 2736-2748, ISSN 1759-6653
Wydawca: Oxford University Press
DOI: 10.1093/gbe/evy205

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

Autorzy: Schön, Max E.; Eme, Laura; Ettema, Thijs J.G.
Opublikowane w: Bioinformatics, Numer 36(6), 2019, Strona(/y) 1718–1724, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1101/688465

Single cell ecology

Autorzy: Thomas A. Richards, Ramon Massana, Stefano Pagliara, Neil Hall
Opublikowane w: Philosophical Transactions of the Royal Society B: Biological Sciences, Numer 374/1786, 2019, Strona(/y) 20190076, ISSN 0962-8436
Wydawca: Royal Society of London
DOI: 10.1098/rstb.2019.0076

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

Autorzy: 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
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 117/5, 2020, Strona(/y) 2551-2559, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1910060117

Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

Autorzy: 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
Opublikowane w: Open Biology, Numer 8/1, 2018, Strona(/y) 170184, ISSN 2046-2441
Wydawca: Royal Society Publishing
DOI: 10.1098/rsob.170184

Genome Resolved Biogeography of Mamiellales

Autorzy: Jade Leconte, L. Felipe Benites, Thomas Vannier, Patrick Wincker, Gwenael Piganeau, Olivier Jaillon
Opublikowane w: Genes, Numer 11/1, 2020, Strona(/y) 66, ISSN 2073-4425
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes11010066

Disentangling the mechanisms shaping the surface ocean microbiota

Autorzy: 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
Opublikowane w: Microbiome, 2020, ISSN 2049-2618
Wydawca: BioMed Central Ltd.
DOI: 10.21203/rs.2.17228/v2

Identity Noise and Adipogenic Traits Characterize Dermal Fibroblast Aging

Autorzy: 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
Opublikowane w: Cell, Numer 175/6, 2018, Strona(/y) 1575-1590.e22, ISSN 0092-8674
Wydawca: Cell Press
DOI: 10.1016/j.cell.2018.10.012

Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates

Autorzy: Aurelie Labarre, Aleix Obiol, Susanne Wilken, Irene Forn, Ramon Massana
Opublikowane w: Limnology and Oceanography, Numer 65/S1, 2020, ISSN 0024-3590
Wydawca: American Society of Limnonogy and Oceanography
DOI: 10.1002/lno.11379

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

Autorzy: 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
Opublikowane w: PLOS Pathogens, Numer 16/2, 2020, Strona(/y) e1008107, ISSN 1553-7374
Wydawca: Public Library of Science
DOI: 10.1371/journal.ppat.1008107

Virus-host coexistence in phytoplankton through the genomic lens

Autorzy: 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
Opublikowane w: Science Advances, Numer 6/14, 2020, Strona(/y) eaay2587, ISSN 2375-2548
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/sciadv.aay2587

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

Autorzy: Atefeh Lafzi, Catia Moutinho, Simone Picelli, Holger Heyn
Opublikowane w: Nature Protocols, Numer 13/12, 2018, Strona(/y) 2742-2757, ISSN 1754-2189
Wydawca: 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

Autorzy: Konstantina Mitsi, Alicia S. Arroyo, Iñaki Ruiz-Trillo
Opublikowane w: Biology Letters, Numer 15/9, 2019, Strona(/y) 20190182, ISSN 1744-9561
Wydawca: The Royal Society
DOI: 10.1098/rsbl.2019.0182

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

Autorzy: Yaiza M. Castillo, Jean‐François Mangot, Luiz Felipe Benites, Ramiro Logares, Megumi Kuronishi, Hiroyuki Ogata, Olivier Jaillon, Ramon Massana, Marta Sebastián, Dolors Vaqué
Opublikowane w: Molecular Ecology, Numer 28/18, 2019, Strona(/y) 4272-4289, ISSN 0962-1083
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/mec.15210

Linking metagenomics to aquatic microbial ecology and biogeochemical cycles

Autorzy: Hans‐Peter Grossart, Ramon Massana, Katherine D. McMahon, David A. Walsh
Opublikowane w: Limnology and Oceanography, Numer 65/S1, 2020, ISSN 0024-3590
Wydawca: American Society of Limnonogy and Oceanography
DOI: 10.1002/lno.11382

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

Autorzy: 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
Opublikowane w: Nature Biotechnology, Numer 38/6, 2020, Strona(/y) 747-755, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-020-0469-4

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

Autorzy: Naoji Yubuki, Luis Javier Galindo, Guillaume Reboul, Purificación López-García, Matthew W Brown, Nicolas Pollet, David Moreira
Opublikowane w: Molecular Biology and Evolution, Numer 37/3, 2019, Strona(/y) 651-659, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msz250

Uncovering microbial inter-domain interactions in complex communities

Autorzy: Javier Florenza, Manu Tamminen, Stefan Bertilsson
Opublikowane w: Philosophical Transactions of the Royal Society B: Biological Sciences, Numer 374/1786, 2019, Strona(/y) 20190087, ISSN 0962-8436
Wydawca: 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

Autorzy: Luis Javier Galindo, Guifré Torruella, David Moreira, Yana Eglit, Alastair G. B. Simpson, Eckhard Völcker, Steffen Clauß, Purificación López-García
Opublikowane w: Philosophical Transactions of the Royal Society B: Biological Sciences, Numer 374/1786, 2019, Strona(/y) 20190094, ISSN 0962-8436
Wydawca: Royal Society of London
DOI: 10.1098/rstb.2019.0094

Gene space completeness in complex plant genomes

Autorzy: Michiel Van Bel, François Bucchini, Klaas Vandepoele
Opublikowane w: Current Opinion in Plant Biology, Numer 48, 2019, Strona(/y) 9-17, ISSN 1369-5266
Wydawca: 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

Autorzy: 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
Opublikowane w: Genome Biology and Evolution, Numer 10/9, 2018, Strona(/y) 2347-2365, ISSN 1759-6653
Wydawca: Oxford University Press
DOI: 10.1093/gbe/evy167

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

Autorzy: Oriol Canals, Aleix Obiol, Imer Muhovic, Dolors Vaqué, Ramon Massana
Opublikowane w: Molecular Ecology, Numer 29/15, 2020, Strona(/y) 2824-2839, ISSN 0962-1083
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/mec.15528