Access content directly

Patrick Wincker

439
Documents
Current affiliations
  • 1179758
Researcher identifiers

Publications

Sea surface temperature reconstruction in the Pacific Ocean using multi-elemental proxy in Porites and Diploastrea corals: Application to Palau Archipelago

Marine Canesi , Éric Douville , Paolo Montagna , Louise Bordier , Sandrine Caquineau
Chemical Geology, 2024, 645, pp.121884. ⟨10.1016/j.chemgeo.2023.121884⟩
Journal articles hal-04337163v1
Image document

Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions

Clemens Schauberger , Bo Thamdrup , Clarisse Lemonnier , Blandine Trouche , Julie Poulain
ISME Communications, 2024, 4 (1), pp.ycad005. ⟨10.1093/ismeco/ycad005⟩
Journal articles hal-04492228v1
Image document

Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

Ana Paula Zotta Mota , Georgios Koutsovoulos , Laetitia Perfus-Barbeoch , Evelin Despot-Slade , Karine Labadie
Nature Communications, 2024, 15 (1), pp.773. ⟨10.1038/s41467-024-44914-y⟩
Journal articles hal-04489824v1
Image document

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Corentin Hochart , Lucas Paoli , Hans-Joachim Ruscheweyh , Guillem Salazar , Emilie Boissin
Nature Communications, 2023, 14 (1), pp.3037. ⟨10.1038/s41467-023-38502-9⟩
Journal articles hal-04176293v1
Image document

Different environmental response strategies in sympatric corals from Pacific Islands

Barbara Porro , Thamilla Zamoum , Didier Forcioli , Eric Gilson , Adrien Poquet
Communications Earth & Environment, 2023, 4 (1), pp.311. ⟨10.1038/s43247-023-00946-8⟩
Journal articles hal-04205154v1
Image document

Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean

Maggie M Reddy , Corentine Goossens , Yuxiang Zhou , Slimane Chaib , Delphine Raviglione
Communications Earth & Environment, 2023, 4 (1), pp.281. ⟨10.1038/s43247-023-00942-y⟩
Journal articles hal-04184949v1
Image document

Host transcriptomic plasticity and photosymbiotic fidelity underpin $Pocillopora$ acclimatization across thermal regimes in the Pacific Ocean

Eric J Armstrong , Julie Lê-Hoang , Quentin Carradec , Jean-Marc Aury , Benjamin Noel
Nature Communications, 2023, 14, pp.3056. ⟨10.1038/s41467-023-38610-6⟩
Journal articles cea-04171796v1
Image document

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

Hugo Doré , Ulysse Guyet , Jade Leconte , Gregory Farrant , Benjamin Alric
The International Society of Microbiologial Ecology Journal, 2023, 17 (5), pp.720-732. ⟨10.1038/s41396-023-01386-0⟩
Journal articles hal-04238382v1
Image document

Pervasive tandem duplications and convergent evolution shape coral genomes

Benjamin Noel , France Denoeud , Alice Rouan , Carol Buitrago-López , Laura Capasso
Genome Biology, 2023, 24 (1), pp.123. ⟨10.1186/s13059-023-02960-7⟩
Journal articles hal-04117388v1

Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood

Stefanie Wagner , Andaine Seguin-Orlando , Jean-Charles Leplé , Thibault Leroy , Céline Lalanne
Molecular Ecology, 2023, ⟨10.1111/mec.16859⟩
Journal articles hal-04158430v1

Pan-Arctic plankton community structure and its global connectivity

Federico Ibarbalz , Nicolas Henry , Frédéric Mahé , Mathieu Ardyna , Adriana Zingone
Elementa: Science of the Anthropocene, 2023, 11 (1), ⟨10.1525/elementa.2022.00060⟩
Journal articles hal-04295751v1
Image document

Predicting global distributions of eukaryotic plankton communities from satellite data

Hiroto Kaneko , Hisashi Endo , Nicolas Henry , Cédric Berney , Frédéric Mahé
ISME Communications, 2023, 3 (1), pp.101. ⟨10.1038/s43705-023-00308-7⟩
Journal articles hal-04394784v1
Image document

Differences in carbonate chemistry up-regulation of long-lived reef-building corals

Marine Canesi , Éric Douville , Paolo Montagna , Marco Taviani , Jarosław Stolarski
Scientific Reports, 2023, 13 (1), pp.11589. ⟨10.1038/s41598-023-37598-9⟩
Journal articles cea-04170119v1
Image document

Ocean-wide comparisons of mesopelagic planktonic community structures

Janaina Rigonato , Marko Budinich , Alejandro Murillo , Manoela Brandão , Juan Pierella Karlusich
ISME Communications, 2023, 3 (1), pp.83. ⟨10.1038/s43705-023-00279-9⟩
Journal articles hal-04184772v1
Image document

Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Fabien Lombard , Guillaume Bourdin , Stéphane Pesant , Sylvain Agostini , Alberto Baudena
Scientific Data , 2023, 10 (1), pp.324. ⟨10.1038/s41597-022-01757-w⟩
Journal articles hal-04164118v1
Image document

Mission Tara Microplastics: a holistic set of protocols and data resources for the field investigation of plastic pollution along the land-sea continuum in Europe

Jean-François Ghiglione , Valérie Barbe , Stéphane Bruzaud , Gaëtan Burgaud , Jérôme Cachot
Environmental Science and Pollution Research, 2023, ⟨10.1007/s11356-023-26883-9⟩
Journal articles hal-04302147v1
Image document

Imputed genomes of historical horses provide insights into modern breeding

Evelyn T Todd , Aurore Fromentier , Richard Sutcliffe , Yvette Running , Horse Collin
iScience, 2023, 26 (7), pp.107104. ⟨10.1016/j.isci⟩
Journal articles hal-04242127v1
Image document

Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation

Isabel Sanz-Sáez , Pablo Sánchez , Guillem Salazar , Shinichi Sunagawa , Colomban de Vargas
ISME Communications, 2023, 3 (1), ⟨10.1038/s43705-023-00290-0⟩
Journal articles cea-04481824v1
Image document

Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes

Ferdinand Marlétaz , Arnaud Couloux , Julie Poulain , Karine Labadie , Corinne da Silva
Cell Genomics, 2023, 3 (4), pp.100295. ⟨10.1016/j.xgen.2023.100295⟩
Journal articles hal-04093287v1
Image document

Diversity of the Pacific Ocean coral reef microbiome

Pierre Galand , Hans-Joachim Ruscheweyh , Guillem Salazar , Corentin Hochart , Nicolas Henry
Nature Communications, 2023, 14 (1), pp.3039. ⟨10.1038/s41467-023-38500-x⟩
Journal articles hal-04176291v1

Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments

Blandine Trouche , Clemens Schauberger , Feriel Bouderka , Jean-Christophe Auguet , Caroline Belser
ISME Communications, 2023, 3 (1), pp.133. ⟨10.1038/s43705-023-00341-6⟩
Journal articles hal-04388214v1

Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

Richard Dorrell , Alan Kuo , Zoltan Füssy , Elisabeth Richardson , Asaf Salamov
Life Science Alliance, 2023, 6 (3), pp.e202201833. ⟨10.26508/lsa.202201833⟩
Journal articles cea-04321515v1
Image document

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Caroline Belser , Julie Poulain , Karine Labadie , Frederick Gavory , Adriana Alberti
Scientific Data , 2023, 10 (1), pp.326. ⟨10.1038/s41597-023-02204-0⟩
Journal articles hal-04176297v1
Image document

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Alex Veglia , Kalia Bistolas , Christian Voolstra , Benjamin Hume , Hans-Joachim Ruscheweyh
Communications Biology, 2023, 6 (1), pp.566. ⟨10.1038/s42003-023-04917-9⟩
Journal articles hal-04176296v1
Image document

Pan-Arctic plankton community structure and its global connectivity

Federico M Ibarbalz , Nicolas Henry , Frédéric Mahé , Mathieu Ardyna , Adriana Zingone
Elementa: Science of the Anthropocene, 2023, 11 (1), pp.00060. ⟨10.1525/elementa.2022.00060⟩
Journal articles hal-04267640v1
Image document

DNA methylation-based profiling of horse archaeological remains for age-at-death and castration

Xuexue Liu , Andaine Seguin- Orlando , Lorelei Chauvey , Gaëtan Tressières , Laure Tonasso-Calvie
iScience, 2023, 26 (3), pp.106144. ⟨10.1016/j.isci.2023.106144⟩
Journal articles cea-04286440v1
Image document

Early dispersal of domestic horses into the Great Plains and northern Rockies

William Timothy Treal Taylor , Pablo Librado , Mila Hunska Tašunke Icu , Carlton Shield Chief Gover , Jimmy Arterberry
Science, 2023, 379 (6639), pp.1316-1323. ⟨10.1126/science.adc9691⟩
Journal articles hal-04065852v1
Image document

Mirusviruses link herpesviruses to giant viruses

Morgan Gaïa , Lingjie Meng , Eric Pelletier , Patrick Forterre , Chiara Vanni
Nature, 2023, 616 (7958), pp.783-789. ⟨10.1038/s41586-023-05962-4⟩
Journal articles pasteur-04085734v1
Image document

Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Alice Rouan , Melanie Pousse , Nadir Djerbi , Barbara Porro , Guillaume Bourdin
Nature Communications, 2023, 14 (1), pp.3038. ⟨10.1038/s41467-023-38499-1⟩
Journal articles cea-04171809v1
Image document

Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Christian R Voolstra , Benjamin C C Hume , Eric J Armstrong , Guinther Mitushasi , Barbara Porro
npj Biodiversity, 2023, 2 (1), pp.15. ⟨10.1038/s44185-023-00020-8⟩
Journal articles hal-04157744v1
Image document

Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei

Adrien Tran Y. Lu , Stephanie Ruault , Claire Daguin-Thiébaut , Jade Castel , Nicolas Bierne
Molecular Ecology, 2022, 31 (10), pp.2796-2813. ⟨10.1111/mec.16430⟩
Journal articles hal-03669635v1
Image document

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

Ahmed Zayed , James Wainaina , Guillermo Dominguez-Huerta , Eric Pelletier , Jiarong Guo
Science, 2022, 376 (6589), pp.156-162. ⟨10.1126/science.abm5847⟩
Journal articles hal-03781924v1
Image document

Diversity and ecological footprint of Global Ocean RNA viruses

Guillermo Dominguez-Huerta , Ahmed Zayed , James Wainaina , Jiarong Guo , Funing Tian
Science, 2022, 376 (6598), pp.1202-1208. ⟨10.1126/science.abn6358⟩
Journal articles hal-03781935v1
Image document

Genomic adaptation of the picoeukaryote $Pelagomonas\ calceolata$ to iron-poor oceans revealed by a chromosome-scale genome sequence

Nina Guérin , Marta Ciccarella , Elisa Flamant , Paul Frémont , Sophie Mangenot
Communications Biology, 2022, 5 (1), pp.983. ⟨10.1038/s42003-022-03939-z⟩
Journal articles cea-03791710v1
Image document

Priorities for ocean microbiome research

Andre Abreu , Etienne Bourgois , Adam Gristwood , Romain Troublé , Silvia Acinas
Nature Microbiology, 2022, 7 (7), pp.937-947. ⟨10.1038/s41564-022-01145-5⟩
Journal articles hal-03781942v1
Image document

Diversity and evolution of pigment types in marine $Synechococcus$ cyanobacteria

Théophile Grébert , Laurence Garczarek , Vincent Daubin , Florian Humily , Dominique Marie
Genome Biology and Evolution, 2022, 14 (4), pp.evac035. ⟨10.1093/gbe/evac035⟩
Journal articles hal-03641745v1

Author Correction: Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Yucheng Wang , Mikkel Winther Pedersen , Inger Greve Alsos , Bianca de Sanctis , Fernando Racimo
Nature, 2022, 603, pp.E31-E31. ⟨10.1038/s41586-022-04628-x⟩
Journal articles insu-03745285v1
Image document

Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

Richard Dorrell , Alan Kuo , Zoltan Füssy , Elisabeth Richardson , Asaf Salamov
Life Science Alliance, 2022, 6 (3), pp.e202201833. ⟨10.26508/lsa.202201833⟩
Journal articles hal-03859139v1
Image document

Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Tristan Cordier , Inès Barrenechea Angeles , Nicolas Henry , Franck Lejzerowicz , Cédric Berney
Science Advances , 2022, 8 (5), ⟨10.1126/sciadv.abj9309⟩
Journal articles hal-03561462v1

High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change

Sandra Garcés-Pastor , Eric Coissac , Sébastien Lavergne , Christoph Schwörer , Jean-Paul Theurillat
Nature Communications, 2022, 13 (1), pp.6559. ⟨10.1038/s41467-022-34010-4⟩
Journal articles hal-04387667v1
Image document

Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France

Benoît Clavel , Sébastien Lepetz , Loreleï Chauvey , Stéphanie Schiavinato , Laure Tonasso-Calvière
Journal of Archaeological Science: Reports, 2022, 41, pp.103341. ⟨10.1016/j.jasrep.2022.103341⟩
Journal articles halshs-03755076v1

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

Ahmed Zayed , James Wainaina , Guillermo Dominguez-Huerta , Eric Pelletier , Jiarong Guo
Science, 2022, 376 (6589), pp.156-162. ⟨10.1126/science.abm5847⟩
Journal articles hal-03872940v1
Image document

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Daniel Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont
eLife, 2022, 11, pp.e78129. ⟨10.7554/eLife.78129⟩
Journal articles hal-02399723v2
Image document

A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Juan José Pierella Karlusich , Eric Pelletier , Lucie Zinger , Fabien Lombard , Adriana Zingone
Molecular Ecology Resources, 2022, 23 (1), pp.16-40. ⟨10.1111/1755-0998.13592⟩
Journal articles hal-03559541v1
Image document

The genomic history and global expansion of domestic donkeys

Evelyn Todd , Laure Tonasso-Calvière , Loreleï Chauvey , Stéphanie Schiavinato , Antoine Fages
Science, 2022, 377 (6611), pp.1172-1180. ⟨10.1126/science.abo3503⟩
Journal articles hal-03827857v1

ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications

Charles Pouchon , Frédéric Boyer , Cristina Roquet , France Denoeud , Jérome Chave
Molecular Ecology Resources, 2022, 22 (5), pp.2018-2037. ⟨10.1111/1755-0998.13584⟩
Journal articles hal-03839343v1

Biosynthetic potential of the global ocean microbiome

Lucas Paoli , Hans-Joachim Ruscheweyh , Clarissa Forneris , Florian Hubrich , Satria Kautsar
Nature, 2022, 607 (7917), pp.111-118. ⟨10.1038/s41586-022-04862-3⟩
Journal articles hal-04376240v1

Reply to: When did mammoths go extinct?

Yucheng Wang , Ana Prohaska , Haoran Dong , Adriana Alberti , Inger Greve Alsos
Nature, 2022, 612 (7938), pp.E4-E6. ⟨10.1038/s41586-022-05417-2⟩
Journal articles hal-04242151v1
Image document

Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection

Aurélie Canaguier , Romane Guilbaud , Erwan Denis , Ghislaine Magdelenat , Caroline Belser
BMC Genomics, 2022, 23 (1), pp.317. ⟨10.1186/s12864-022-08499-4⟩
Journal articles hal-03977388v1
Image document

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

Jean-Marc Aury , Stefan Engelen , Benjamin Istace , Cécile Monat , Pauline Lasserre-Zuber
GigaScience, 2022, 11, pp.1-18. ⟨10.1093/gigascience/giac034⟩
Journal articles hal-03658639v1

Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans

Naama Lang-Yona , J. Michel Flores , Rotem Haviv , Adriana Alberti , Julie Poulain
Communications Earth & Environment, 2022, 3 (1), pp.121. ⟨10.1038/s43247-022-00441-6⟩
Journal articles hal-04382382v1
Image document

Restructuring of plankton genomic biogeography in the surface ocean under climate change

Paul Frémont , Marion Gehlen , Mathieu Vrac , Jade Leconte , Tom O. Delmont
Nature Climate Change, 2022, 12 (4), pp.393-401. ⟨10.1038/s41558-022-01314-8⟩
Journal articles insu-03659872v1

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Tom Delmont , Morgan Gaia , Damien Hinsinger , Paul Frémont , Chiara Vanni
Cell Genomics, 2022, 2 (5), pp.100123. ⟨10.1016/j.xgen.2022.100123⟩
Journal articles hal-03872935v2
Image document

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Sarah Farhat , Phuong Le , Ehsan Kayal , Benjamin Noel , Estelle Bigeard
BMC Biology, 2021, 19 (1), ⟨10.1186/s12915-020-00927-9⟩
Journal articles hal-03114990v1
Image document

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Yucheng Wang , Mikkel Winther Pedersen , Inger Greve Alsos , Bianca de Sanctis , Fernando Racimo
Nature, 2021, 598 (7882), pp.634-640. ⟨10.1038/s41586-021-04016-x⟩
Journal articles hal-03431961v1
Image document

Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Elise J Gay , Jessica L Soyer , Nicolas Lapalu , Juliette Linglin , Isabelle Fudal
BMC Biology, 2021, 19 (1), pp.e041118. ⟨10.1186/s12915-021-00989-3⟩
Journal articles hal-03190704v1
Image document

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

Benjamin Istace , Caroline Belser , Cyril Falentin , Karine Labadie , Franz Boideau
Biology, 2021, 10 (8), ⟨10.3390/biology10080732⟩
Journal articles hal-03318024v1
Image document

Diversity and biogeography of bathyal and abyssal seafloor bacteria and archaea along a Mediterranean-Atlantic gradient

Blandine Trouche , Miriam Brandt , Caroline Belser , Covadonga Orejas , Stephane Pesant
Frontiers in Microbiology, 2021, 12, pp.702016. ⟨10.3389/fmicb.2021.702016⟩
Journal articles hal-03589735v1
Image document

Population genomics of apricots unravels domestication history and adaptive events

Alexis Groppi , Shuo Liu , A. Cornille , David Tricon , Quynh Trang Bui
Nature Communications, 2021, 12 (1), pp.3956. ⟨10.1038/s41467-021-24283-6⟩
Journal articles hal-03282504v1
Image document

Historical management of equine resources in France from the Iron Age to the Modern Period

Sébastien Lepetz , Benoît Clavel , Duha Alioğlu , Lorelei Chauvey , Stéphanie Schiavinato
Journal of Archaeological Science: Reports, 2021, 40 (B), pp.103250. ⟨10.1016/j.jasrep.2021.103250⟩
Journal articles hal-03431948v1
Image document

The origins and spread of domestic horses from the Western Eurasian steppes

Pablo Librado , Naveed Khan , Antoine Fages , Mariya A Kusliy , Tomasz Suchan
Nature, 2021, 598 (7882), pp.634-640. ⟨10.1038/s41586-021-04018-9⟩
Journal articles hal-03425363v1

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

Tom Delmont , Juan José Pierella Karlusich , Iva Veseli , Jessika Fuessel , A. Murat Eren
The International Society of Microbiologial Ecology Journal, 2021, 16 (4), pp.927-936. ⟨10.1038/s41396-021-01135-1⟩
Journal articles hal-03480646v1

Author Correction: A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Quentin Carradec , Julie Poulain , Emilie Boissin , Benjamin Hume , Christian Voolstra
Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-81544-6⟩
Journal articles hal-03368783v1
Image document

Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

Marta Royo-Llonch , Pablo Sánchez , Clara Ruiz-González , Guillem Salazar , Carlos Pedrós-Alió
Nature Microbiology, 2021, 6 (12), pp.1561-1574. ⟨10.1038/s41564-021-00979-9⟩
Journal articles hal-03781908v1
Image document

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients.

Clemens Schauberger , Ronnie N. Glud , Bela Hausmann , Blandine Trouche , Lois Maignien
The International Society of Microbiologial Ecology Journal, In press, ⟨10.1038/s41396-021-01021-w⟩
Journal articles hal-03415694v1

Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding

Miriam Brandt , Blandine Trouche , Laure Quintric , Babett Günther , Patrick Wincker
Molecular Ecology Resources, 2021, 21 (6), pp.1904-1921. ⟨10.1111/1755-0998.13398⟩
Journal articles hal-04203425v1
Image document

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

Miriam I Brandt , Florence Pradillon , Blandine Trouche , Nicolas Henry , Cathy Liautard-Haag
Scientific Reports, 2021, 11 (1), pp.7856. ⟨10.1038/s41598-021-86396-8⟩
Journal articles hal-03198097v1
Image document

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

Caroline Belser , Franc-Christophe Baurens , Benjamin Noel , Guillaume Martin , Corinne Cruaud
Communications Biology, 2021, 4 (1), ⟨10.1038/s42003-021-02559-3⟩
Journal articles hal-03352701v1
Image document

Environmental vulnerability of the global ocean epipelagic plankton community interactome

Samuel Chaffron , Erwan Delage , Marko Budinich , Damien Vintache , Nicolas Henry
Science Advances , 2021, 7 (35), pp.eabg1921. ⟨10.1126/sciadv.abg1921⟩
Journal articles hal-03443359v2
Image document

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Laurence Garczarek , Ulysse Guyet , Hugo Doré , Gregory Farrant , Mark Hoebeke
Nucleic Acids Research, 2021, 49 (D1), pp.D667-D676. ⟨10.1093/nar/gkaa958⟩
Journal articles hal-02988562v1
Image document

Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids

Pierre Clavel , Jean Dumoncel , Clio Der Sarkissian , Andaine Seguin-Orlando , Laure Calvière-Tonasso
Journal of Archaeological Science, 2021, 131, pp.105383. ⟨10.1016/j.jas.2021.105383⟩
Journal articles hal-03413040v1
Image document

Male differentiation in the marine Copepod Oithona nana reveals the development of a new nervous ganglion and Lin12-Notch-repeat protein-associated proteolysis

Kevin Sugier , Romuald Laso-Jadart , Benoît Vacherie , Jos Käfer , Laurie Bertrand
Biology, 2021, 10 (7), pp.657. ⟨10.3390/biology10070657⟩
Journal articles hal-03286235v1
Image document

Macroscale patterns of oceanic zooplankton composition and size structure

Manoela Brandão , Fabio Benedetti , Séverine Martini , Yawouvi Dodji Soviadan , Jean-Olivier Irisson
Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-94615-5⟩
Journal articles hal-03318806v1
Image document

Comparative genomics reveals new functional insights in uncultured MAST species

Aurelie Labarre , David López-Escardó , Francisco Latorre , Guy Leonard , François Bucchini
The International Society of Microbiologial Ecology Journal, 2021, 15 (6), pp.1767-1781. ⟨10.1038/s41396-020-00885-8⟩
Journal articles hal-04288985v1
Image document

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Juan José Pierella Karlusich , Eric Pelletier , Fabien Lombard , Madeline Carsique , Etienne Dvorak
Nature Communications, 2021, 12, pp.4160. ⟨10.1038/s41467-021-24299-y⟩
Journal articles hal-03334117v2

Author Correction: Macroscale patterns of oceanic zooplankton composition and size structure

Manoela Brandão , Fabio Benedetti , Séverine Martini , Yawouvi Dodji Soviadan , Jean-Olivier Irisson
Scientific Reports, 2021, 11 (1), pp.20226. ⟨10.1038/s41598-021-99772-1⟩
Journal articles hal-04394798v1
Image document

An assessment of environmental metabarcoding protocols aiming at favoring contemporary biodiversity in inventories of deep-sea communities

Miriam Brandt , Blandine Trouche , Nicolas Henry , Cathy Liautard-Haag , Lois Maignien
Frontiers in Marine Science, 2020, 7, pp.234. ⟨10.3389/fmars.2020.00234⟩
Journal articles hal-03410860v1
Image document

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Quentin Carradec , Julie Poulain , Emilie Boissin , Benjamin Hume , Christian Voolstra
Scientific Reports, 2020, 10 (1), pp.15893. ⟨10.1038/s41598-020-72589-0⟩
Journal articles hal-02964556v1
Image document

Long-read assembly of the Brassica napus reference genome Darmor-bzh

Mathieu Rousseau-Gueutin , Caroline Belser , Corinne Da silva , Gautier Richard , Benjamin Istace
GigaScience, 2020, 9 (12), pp.giaa137. ⟨10.1093/gigascience/giaa137⟩
Journal articles hal-03283975v1
Image document

Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics

Alexey Vorobev , Marion Dupouy , Quentin Carradec , Tom O. Delmont , Anita Annamalé
Genome Research, 2020, 30 (4), pp.647-659. ⟨10.1101/gr.253070.119⟩
Journal articles hal-02573621v1
Image document

Genome Resolved Biogeography of Mamiellales

Jade Leconte , L. Felipe Felipe Benites , Thomas Vannier , Patrick Wincker , Gwenael Piganeau
Genes, 2020, 11 (1), pp.66. ⟨10.3390/genes11010066⟩
Journal articles hal-02505108v1
Image document

Tara Pacific Expedition’s Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans: Overview and Preliminary Results

J. Flores , G. Bourdin , O. Altaratz , M. Trainic , N. Lang-Yona
Bulletin of the American Meteorological Society, 2020, 101 (5), pp.E536-E554. ⟨10.1175/BAMS-D-18-0224.1⟩
Journal articles hal-02967981v1

Tara Oceans: towards global ocean ecosystems biology

Shinichi Sunagawa , Silvia Acinas , Peer Bork , Chris Bowler , Silvia Acinas
Nature Reviews Microbiology, 2020, 18 (8), pp.428-445. ⟨10.1038/s41579-020-0364-5⟩
Journal articles hal-04394809v1
Image document

Le RMQS au service de l'écologie microbienne des sols français

Samuel S. Dequiedt , Battle Karimi , Nicolas Chemidlin Prévost-Bouré , Sébastien Terrat , Walid Horrigue
Étude et Gestion des Sols, 2020, 27 (1), pp.51-71
Journal articles hal-02540019v1
Image document

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Hugo Doré , Gregory Farrant , Ulysse Guyet , Julie Haguait , Florian Humily
Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.567431⟩
Journal articles hal-02938656v1

Biogeography of soil microbial habitats across France

Battle Karimi , Jean Villerd , Samuel Dequiedt , Sébastien Terrat , Nicolas Chemidlin Prévost-Bouré
Global Ecology and Biogeography, 2020, 29 (8), pp.1399-1411. ⟨10.1111/geb.13118⟩
Journal articles hal-03014310v1
Image document

Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)

Romuald Laso‐jadart , Kevin Sugier , Emmanuelle Petit , Karine Labadie , Pierre Peterlongo
Ecology and Evolution, 2020, 10 (16), pp.8894-8905. ⟨10.1002/ece3.6588⟩
Journal articles hal-02999798v1

Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions

Hisashi Endo , Romain Blanc Mathieu , Yanze Li , Guillem Salazar , Nicolas Henry
Nature Ecology & Evolution, 2020, 4 (12), pp.1639-1649. ⟨10.1038/s41559-020-01288-w⟩
Journal articles hal-02974168v1
Image document

Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

Shinya Sato , Deepak Nanjappa , Richard G Dorrell , Fabio Rocha Jimenez Vieira , Elena Kazamia
Scientific Reports, 2020, 10 (1), pp.9449. ⟨10.1038/s41598-020-65941-x⟩
Journal articles inserm-02886223v1

BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons

Christophe Djemiel , Samuel Dequiedt , Battle Karimi , Aurélien Cottin , Thibault Girier
BMC Bioinformatics, 2020, 21 (1), pp.1-21. ⟨10.1186/s12859-020-03829-3⟩
Journal articles hal-03014150v1

Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability

Paolo Sordino , Salvatore d'Aniello , Eric Pelletier , Patrick Wincker , Valeria Nittoli
Molecular Ecology, 2019, 29 (2), pp.292-307. ⟨10.1111/mec.15321⟩
Journal articles hal-03955981v1

A thousand plants' phylogeny

Patrick Wincker
Nature Plants, 2019, 5 (11), pp.1106-1107. ⟨10.1038/s41477-019-0555-0⟩
Journal articles cea-04309470v1
Image document

The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

Lucas R Leclère , Coralie Horin , Sandra Chevalier , Pascal Lapébie , Philippe Dru
Nature Ecology & Evolution, 2019, 3 (5), pp.801-810. ⟨10.1038/s41559-019-0833-2⟩
Journal articles hal-02115215v1
Image document

Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity

Battle Karimi , Samuel S. Dequiedt , Sébastien Terrat , Claudy C. Jolivet , Dominique D. Arrouays
Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-40422-y⟩
Journal articles hal-02093081v1
Image document

Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)

Gabriel Gorsky , Guillaume Bourdin , Fabien Lombard , Maria Luiza Pedrotti , Samuel Audrain
Frontiers in Marine Science, 2019, 6, pp.650. ⟨10.3389/fmars.2019.00750⟩
Journal articles hal-02407578v1
Image document

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean

Serge Planes , Denis Allemand , Sylvain Agostini , Bernard Banaigs , Emilie Boissin
PLoS Biology, 2019, 17 (9), pp.e3000483. ⟨10.1371/journal.pbio.3000483⟩
Journal articles hal-02402685v1
Image document

Marine DNA viral macro- and microdiversity from Pole to Pole

Ann Gregory , Ahmed Zayed , Nádia Conceição-Neto , Ben Temperton , Ben Bolduc
Cell, 2019, 177 (5), pp.1109-1123.e14. ⟨10.1016/j.cell.2019.03.040⟩
Journal articles hal-02387010v1
Image document

Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Julie Ferreira de Carvalho , Jérémy Lucas , Gwenaëlle Deniot , Cyril Falentin , Olivier Filangi
Plant Journal, 2019, 98 (3), pp.434-447. ⟨10.1111/tpj.14228⟩
Journal articles hal-02019346v1

A reference genome for pea provides insight into legume genome evolution

Jonathan J. Kreplak , Mohammed-Amin Madoui , Petr Cápal , Petr Novak , Karine Labadie
Nature Genetics, 2019, 51 (9), pp.1411-1422. ⟨10.1038/s41588-019-0480-1⟩
Journal articles hal-02278272v1
Image document

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

M. E Sieracki , N. J Poulton , O. Jaillon , P. Wincker , Colomban de Vargas
Scientific Reports, 2019, 9, pp.6025. ⟨10.1038/s41598-019-42487-1⟩
Journal articles hal-02113815v1
Image document

Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes

Greta Busseni , Fabio Rocha Jimenez Vieira , Alberto Amato , Eric Pelletier , Juan Pierella Karlusich
Molecular Biology and Evolution, 2019, 36 (11), pp.2522-2535. ⟨10.1093/molbev/msz157⟩
Journal articles hal-02184019v1
Image document

Global Trends in Marine Plankton Diversity across Kingdoms of Life

Federico Ibarbalz , Nicolas Henry , Manoela Brandão , Severine Martini , Greta Busseni
Cell, 2019, 179 (5), pp.1084-1097.e21. ⟨10.1016/j.cell.2019.10.008⟩
Journal articles hal-03094778v1
Image document

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Luigi Caputi , Quentin Carradec , Damien Eveillard , Amos Kirilovsky , Eric Pelletier
Global Biogeochemical Cycles, 2019, 33 (3), pp.391-419. ⟨10.1029/2018GB006022⟩
Journal articles hal-02999805v1

A gene graveyard in the genome of the fungus Podospora comata

Philippe Silar , Jean-Marc Dauget , Valérie Gautier , Pierre Grognet , Michelle Chablat
Molecular Genetics and Genomics, 2019, 294 (1), pp.177--190. ⟨10.1007/s00438-018-1497-3⟩
Journal articles hal-02173830v1

Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability

Paolo Sordino , Salvatore d'Aniello , Eric Pelletier , Patrick Wincker , Valeria Nittoli
Molecular Ecology, 2019, 29 (2), pp.292-307. ⟨10.1111/mec.15321⟩
Journal articles hal-04394543v1

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Guillem Salazar , Lucas Paoli , Adriana A. Alberti , Jaime Huerta-Cepas , Hans-Joachim Ruscheweyh
Cell, 2019, 179 (5), pp.1068-1083.e21. ⟨10.1016/j.cell.2019.10.014⟩
Journal articles hal-02964513v1
Image document

Transposition favors the generation of large effect mutations that may facilitate rapid adaption

Leandro Quadrana , Mathilde Etcheverry , Arthur Gilly , Erwann Caillieux , Mohammed-Amin Madoui
Nature Communications, 2019, 10, ⟨10.1038/s41467-019-11385-5⟩
Journal articles hal-02398702v1
Image document

Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Amoebophrya Strains

Sarah Farhat , Isabelle Florent , Benjamin Noël , Ehsan Kayal , Corinne da Silva
Frontiers in Microbiology, 2018, 9, ⟨10.3389/fmicb.2018.02251⟩
Journal articles hal-02126891v1
Image document

Genome evolution across 1,011 $Saccharomyces\ cerevisiae$ isolates

Jackson Peter , Matteo de Chiara , Anne Friedrich , Jia-Xing Yue , David Pflieger
Nature, 2018, 556 (7701), pp.339 - 344. ⟨10.1038/s41586-018-0030-5⟩
Journal articles cea-01872910v1
Image document

The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond , Jerome Gouzy , Jérémy Just , Hélène Badouin , Marion Verdenaud
Nature Genetics, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩
Journal articles hal-01798003v1
Image document

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Yoann Seeleuthner , Samuel Mondy , Vincent Lombard , Quentin Carradec , Eric Pelletier
Nature Communications, 2018, 9, pp.310. ⟨10.1038/s41467-017-02235-3⟩
Journal articles hal-01771839v1
Image document

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria

Théophile Grébert , Hugo Doré , Frédéric Partensky , Gregory Farrant , Emmanuel Boss
Proceedings of the National Academy of Sciences of the United States of America, 2018, 115 (9), pp.E2010-E2019. ⟨10.1073/pnas.1717069115⟩
Journal articles hal-01772758v1
Image document

Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle

Claude Murat , Thibaut Payen , Benjamin Noël , Alan Kuo , Emmanuelle Morin
Nature Ecology & Evolution, 2018, 2 (12), pp.1956-1965. ⟨10.1038/s41559-018-0710-4⟩
Journal articles hal-02094494v1

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Rudi Appels , Kellye Eversole , Nils Stein , Catherine Feuillet , Beat Keller
Science, 2018, 361 (6403), ⟨10.1126/science.aar7191⟩
Journal articles hal-04198290v1
Image document

Convergent genomic signatures of domestication in sheep and goats

Florian Alberto , Frédéric Boyer , Pablo Orozco-Terwengel , Ian Streeter , Bertrand Servin
Nature Communications, 2018, 9 (1), pp.813. ⟨10.1038/s41467-018-03206-y⟩
Journal articles cea-01875703v1
Image document

A global ocean atlas of eukaryotic genes

Quentin Carradec , Eric Pelletier , Corinne da Silva , Adriana A. Alberti , Yoann Seeleuthner
Nature Communications, 2018, 9 (1), pp.373. ⟨10.1038/s41467-017-02342-1⟩
Journal articles cea-01874711v1
Image document

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

Fabien Dutreux , Corinne da Silva , Léo d'Agata , Arnaud Couloux , Elise Gay
Scientific Data , 2018, 5 (180235), 11 p. ⟨10.1038/sdata.2018.235⟩
Journal articles hal-02621276v1
Image document

Gene flow contributes to diversification of the major fungal pathogen $Candida\ albicans$

Jeanne Ropars , Corinne Maufrais , Dorothée Diogo , Marina Marcet-Houben , Aurélie Perin
Nature Communications, 2018, 9 (1), pp.2253. ⟨10.1038/s41467-018-04787-4⟩
Journal articles pasteur-01815656v1
Image document

A de novo approach to disentangle partner identity and function in holobiont systems

Arnaud Meng , Camille Marchet , Erwan Corre , Pierre Peterlongo , Adriana A. Alberti
Microbiome, 2018, pp.1-35. ⟨10.1186/s40168-018-0481-9⟩
Journal articles hal-01643153v2
Image document

Discovering Millions of Plankton Genomic Markers from the Atlantic Ocean and the Mediterranean Sea

Majda Arif , Jérémy Gauthier , Kevin Sugier , Daniele Iudicone , Olivier Jaillon
Molecular Ecology Resources, 2018, pp.1-24. ⟨10.1111/1755-0998.12985⟩
Journal articles hal-01987200v1

Status of coral reefs of Upolu (Independent State of Samoa) in the South West Pacific and recommendations to promote resilience and recovery of coastal ecosystems

Maren Ziegler , Gaëlle Quéré , Jean-François Ghiglione , Guillaume Iwankow , Valérie Barbe
Marine Pollution Bulletin, 2018, 129 (1), pp.392-398. ⟨10.1016/j.marpolbul.2018.02.044⟩
Journal articles hal-01960450v1

Extracting high molecular weight genomic DNA from Saccharomyces cerevisiae

Erwan Denis , Sophie Sanchez , Barbara Mairey , Odette Beluche , Corinne Cruaud
Protocol Exchange, 2018, ⟨10.1038/protex.2018.076⟩
Journal articles hal-04330988v1
Image document

Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation

Elodie Gaulin , Michiel Pel , Laurent Camborde , Hélène San Clemente , Sarah Courbier
BMC Biology, 2018, 16 (1), ⟨10.1186/s12915-018-0508-5⟩
Journal articles hal-01891875v1

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Rudi Appels , Kellye Eversole , Nils Stein , Catherine Feuillet , Beat Keller
Science, 2018, 361 (6403), ⟨10.1126/science.aar7191⟩
Journal articles hal-04331004v1
Image document

Amphioxus functional genomics and the origins of vertebrate gene regulation

Ferdinand Marletaz , Panos N. Firbas , Ignacio Maeso , Juan J. Tena , Ozren Bogdanovic
Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩
Journal articles hal-02000511v1
Image document

Oak genome reveals facets of long lifespan

Christophe Plomion , Jean-Marc Aury , Joelle Amselem , Thibault Leroy , Florent Murat
Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩
Journal articles hal-01820559v1
Image document

Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy

Kevin Sugier , Benoit Vacherie , Astrid Cornils , Patrick Wincker , Jean-Louis Jamet
PeerJ, 2018, 6, pp.e4685. ⟨10.7717/peerj.4685⟩
Journal articles hal-01979866v1

Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps

Caroline Belser , Benjamin Istace , Erwan Denis , Marion Dubarry , Franc-Christophe Baurens
Nature Plants, 2018, 4 (11), pp.879-887. ⟨10.1038/s41477-018-0289-4⟩
Journal articles hal-01977046v1

Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean

Johan Decelle , Quentin Carradec , Xavier Pochon , Nicolas Henry , Sarah Romac
Current Biology - CB, 2018, 28 (22), pp.3625-3633.e3. ⟨10.1016/j.cub.2018.09.024⟩
Journal articles hal-02194113v1
Image document

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region

Benjamin C C Hume , Maren Ziegler , Julie Poulain , Xavier Pochon , Sarah Romac
PeerJ, 2018, 6, pp.e4816. ⟨10.7717/peerj.4816⟩
Journal articles hal-01822910v1

Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network.

Arnaud Meng , Erwan Corre , Ian Probert , Andres Gutierrez-Rodriguez , Raffaele Siano
Molecular Ecology, 2018, 27 (10), pp.2365-2380. ⟨10.1111/mec.14579⟩
Journal articles hal-02879300v1
Image document

Biogeography of soil bacteria and archaea across France

Battle Karimi , Sébastien Terrat , Samuel S. Dequiedt , Nicolas Saby , Walid Horrigue
Science Advances , 2018, 4 (7), pp.eaat1808. ⟨10.1126/sciadv.aat1808⟩
Journal articles hal-01843961v1

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes

Philippe Cubry , Christine Tranchant-Dubreuil , Anne-Céline Thuillet , Cécile Monat , Marie-Noelle Ndjiondjop
Current Biology - CB, 2018, 28 (14), pp.2274-2282. e6. ⟨10.1016/j.cub.2018.05.066⟩
Journal articles hal-03958213v1
Image document

High-quality $de\ novo$ genome assembly of the $Dekkera\ bruxellensis$ yeast using Nanopore MinION sequencing

Téo Fournier , Jean-Sébastien Gounot , Kelle Freel , Corinne Cruaud , Arnaud Lemainque
G3, 2017, 7 (10), pp.3243-3250. ⟨10.1534/g3.117.300128⟩
Journal articles cea-04315763v1

Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination

Sheng Sun , Vikas Yadav , R. Blake Billmyre , Christina A. Cuomo , Minou Nowrousian
PLoS Biology, 2017, 15 (8), pp.e2002527. ⟨10.1371/journal.pbio.2002527⟩
Journal articles cea-04320302v1
Image document

$de\ novo$ assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

Benjamin Istace , Anne Friedrich , Léo d'Agata , Sébastien Faye , Emilie Payen
Gigascience, 2017, 6 (2), pp.giw018. ⟨10.1093/gigascience/giw018⟩
Journal articles cea-04315750v1
Image document

Mapping and predictive variations of soil bacterial richness across France

Sébastien Terrat , Walid Horrigue , Samuel Dequietd , Nicolas Saby , Mélanie M. Lelievre
PLoS ONE, 2017, 12 (0190128), pp.1-19. ⟨10.1371/journal.pone.0186766⟩
Journal articles hal-01843156v1
Image document

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

Jean-François Mangot , Ramiro Logares , Pablo Sánchez , Fran Latorre , Yoann 6 Seeleuthner
Scientific Reports, 2017, 7, pp.41498. ⟨10.1038/srep41498⟩
Journal articles hal-01466618v1

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona

Mohammed-Amin Madoui , Julie Poulain , Kevin Sugier , Marc Wessner , Benjamin Noel
Molecular Ecology, 2017, 26 (17), pp.4467 - 4482. ⟨10.1111/mec.14214⟩
Journal articles hal-01621969v1
Image document

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Adriana A. Alberti , Julie Poulain , Stefan Engelen , Karine Labadie , Sarah Romac
Scientific Data , 2017, 4, ⟨10.1038/sdata.2017.93⟩
Journal articles hal-01771844v1
Image document

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes

Romain Blanc-Mathieu , Laetitia Zurletto , Jean-Marc Aury , Martine da Rocha , Jerome Gouzy
PLoS Genetics, 2017, 13 (6), pp.e1006777. ⟨10.1371/journal.pgen.1006777⟩
Journal articles hal-01602779v1
Image document

Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination

Sheng Sun , Vikas Yadav , R. Blake Billmyre , Christina A. Cuomo , Minou Nowrousian
PLoS Biology, 2017, 15 (8), pp.e2002527. ⟨10.1371/journal.pbio.2002527⟩
Journal articles cea-04320340v1

High-quality de novo genome assembly of the Dekkera bruxellensis yeast using Nanopore MinION sequencing

Téo Fournier , Jean-Sébastien Gounot , Kelle Freel , Corinne Cruaud , Arnaud Lemainque
G3, 2017, 7 (10), pp.3243-3250. ⟨10.1534/g3.117.300128⟩
Journal articles cea-04315747v1

A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

Roberto Arrigoni , Benoît Vacherie , Francesca Benzoni , Fabrizio Stefani , Eric Karsenti
Molecular Ecology Resources, 2017, 17 (5), pp.1054-1071. ⟨10.1111/1755-0998.12640⟩
Journal articles hal-03971503v1
Image document

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Anaïs Gouin , Anthony Bretaudeau , Kiwoong Nam , Sylvie Gimenez , Jean-Marc Aury
Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩
Journal articles hal-01633879v1

Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis

Petra Spirhanzlova , Sophie Dhorne-Pollet , J.S. Fellah , C. da Silva , T. Tlapakova
Developmental Biology, 2017, 426 (2), pp.255-260. ⟨10.1016/j.ydbio.2016.05.015⟩
Journal articles hal-01607555v1
Image document

Plankton networks driving carbon export in the oligotrophic ocean

Lionel Guidi , Samuel Chaffron , Lucie Bittner , Damien Eveillard , Abdelhalim Larhlimi
Nature, 2016, 532, pp.465-470. ⟨10.1038/nature16942⟩
Journal articles hal-01275276v1
Image document

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

Francisco M. Cornejo-Castillo , Ana M. Cabello , Guillem Salazar , Patricia Sánchez-Baracaldo , Gipsi Lima-Mendez
Nature Communications, 2016, 7, pp.11071. ⟨10.1038/ncomms11071⟩
Journal articles hal-01295207v1
Image document

Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae)

Julie Boutte , Julie Ferreira de Carvalho , Mathieu Rousseau-Gueutin , Julie Poulain , Corinne da Silva
Genome Biology and Evolution, 2016, 8 (9), pp.3030-3044. ⟨10.1093/gbe/evw209⟩
Journal articles hal-01412081v1
Image document

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria

Gregory K. Farrant , Hugo Doré , Francisco M. Cornejo-Castillo , Frédéric Partensky , Morgane Ratin
Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (24), pp.E3365-E3374. ⟨10.1073/pnas.1524865113⟩
Journal articles hal-01331214v1
Image document

Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells

Christo Kole , Naomi Berdugo , Corinne da Silva , Najate Aït-Ali , Géraldine Millet-Puel
PLoS ONE, 2016, 11 (3), pp.e0150758. ⟨10.1371/journal.pone.0150758⟩
Journal articles hal-01292283v1
Image document

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Simon Roux , Jennifer R. Brum , Bas E. Dutilh , Shinichi Sunagawa , Melissa B. Duhaime
Nature, 2016, 537 (7622), pp.689-693. ⟨10.1038/nature19366⟩
Journal articles hal-01376822v1

Insights into global diatom distribution and diversity in the world's ocean

Shruti Malviya , Eleonora Scalco , Stephane Audic , Flora Vincenta , Alaguraj Veluchamy
Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (11), pp.E1516-E1525. ⟨10.1073/pnas.1509523113⟩
Journal articles hal-01545320v1

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

Noan Le Bescot , Frédéric Mahé , Stéphane Audic , Céline Dimier , Marie-Jose Garet
Environmental Microbiology, 2016, 18 (2), pp.609-626. ⟨10.1111/1462-2920.13039⟩
Journal articles hal-01305586v1
Image document

Survey of the green picoalga Bathycoccus genomes in the global ocean

Thomas Vannier , Jade Leconte , Yoann Seeleuthner , Samuel Mondy , Eric Pelletier
Scientific Reports, 2016, 6, pp.37900. ⟨10.1038/srep37900⟩
Journal articles hal-01410203v1
Image document

Benthic protists: the under-charted majority

Dominik Forster , Micah Dunthorn , Fréderic Mahé , John R. Dolan , Stéphane Audic
FEMS Microbiology Ecology, 2016, 92 (8), pp.fiw120. ⟨10.1093/femsec/fiw120⟩
Journal articles hal-01383722v1

Towards the Rose Genome Sequence and Its Use in Research and Breeding

Fabrice Foucher , Laurence Hibrand-Saint Oyant , Latifa Hamama , Soulaiman Sakr , H. Nybom
Acta Horticulturae, 2015, 1064, pp.167-175. ⟨10.17660/ActaHortic.2015.1064.19⟩
Journal articles hal-02630890v1
Image document

Transcriptome analyses to investigate symbiotic relationships between marine protists

Sergio Balzano , Erwan Corre , Johan Decelle , Roberto Sierra , Patrick Wincker
Frontiers in Microbiology, 2015, 6, pp.98. ⟨10.3389/fmicb.2015.00098⟩
Journal articles hal-01143962v1
Image document

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

Guillaume Morel , Lieven Sterck , Dominique Swennen , Marina Marcet-Houben , Djamila Onesime
Scientific Reports, 2015, 5 (1), pp.11571. ⟨10.1038/srep11571⟩
Journal articles hal-03665128v1
Image document

Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

Eric Fontanillas , Michael E Hood , Hélène Badouin , Elsa Petit , Valérie Barbe
Molecular Biology and Evolution, 2015, 32 (4), pp.928-943. ⟨10.1093/molbev/msu396⟩
Journal articles hal-01302682v1
Image document

Patterns and ecological drivers of ocean viral communities

Jennifer Brum , J Cesar Ignacio-Espinoza , Simon Roux , Guilhem Doulcier , Silvia G. Acinas
Science, 2015, 348 (6237), pp.1261498. ⟨10.1126/science.1261498⟩
Journal articles hal-01768331v1

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

Guillaume Morel , Lieven Sterck , Dominique Swennen , Marina Marcet-Houben , Djamila Onesime
Scientific Reports, 2015, 5 (1), ⟨10.1038/srep11571⟩
Journal articles hal-03274350v1
Image document

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

Guillaume Morel , Lieven Sterck , Dominique Swennen , Marina Marcet-Houben , Djamila Onesime
Scientific Reports, 2015, 5, ⟨10.1038/srep11571⟩
Journal articles hal-01201920v1

Tara Oceans studies plankton at PLANETARY SCALE

P. Bork , C. Bowler , Colomban de Vargas , G. Gorsky , E. Karsenti
Science, 2015, 348 (6237), pp.873. ⟨10.1126/science.aac5605⟩
Journal articles hal-01258211v1

Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species

Susete Alves Carvalho , Gregoire G. Aubert , Sebastien Carrere , Corinne Cruaud , Anne-Lise Brochot
Plant Journal, 2015, 84 (1), pp.1-19. ⟨10.1111/tpj.12967⟩
Journal articles hal-02631162v1

Determinants of community structure in the global plankton interactome

Gipsi Lima-Mendez , Karoline Faust , Nicolas Henry , Johan Decelle , Sébastien Colin
Science, 2015, 348 (6237), pp.1262073. ⟨10.1126/science.1262073⟩
Journal articles hal-01234200v1
Image document

Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

Camille Clerissi , Yves Desdevises , Sarah Romac , Stéphane Audic , Colomban de Vargas
Environmental Microbiology Reports, 2015, 7 (6), pp.979-989. ⟨10.1111/1758-2229.12345⟩
Journal articles hal-01246259v1
Image document

Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

Peter von Dassow , Uwe John , Hiroyuki Ogata , Ian Probert , El Mahdi Bendif
The International Society of Microbiologial Ecology Journal, 2015, 9 (6), pp.1365-1377. ⟨10.1038/ismej.2014.221⟩
Journal articles hal-01245155v1

Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides.

Pierre Czernic , Djamel Gully , Fabienne Cartieaux , Lionel Moulin , Ibtissem Guefrachi
Plant Physiology, 2015, 169 (2), pp.1254-65. ⟨10.1104/pp.15.00584⟩
Journal articles hal-01430710v1
Image document

Genome assembly using Nanopore-guided long and error-free DNA reads

Mohammed-Amin Madoui , Stefan Engelen , Corinne Cruaud , Caroline Belser , Laurie Bertrand
BMC Genomics, 2015, 16 (1), pp.327. ⟨10.1186/s12864-015-1519-z⟩
Journal articles hal-04361027v1
Image document

Open science resources for the discovery and analysis of Tara Oceans data

Stéphane Pesant , Fabrice Not , Marc Picheral , Stefanie Kandels-Lewis , Noan Le Bescot
Scientific Data , 2015, 2, pp.150023. ⟨10.1038/sdata.2015.23⟩
Journal articles hal-01253984v1
Image document

Eukaryotic plankton diversity in the sunlit ocean

Noan Le Bescot , Ian Probert , Margaux Carmichael , Julie Poulain , Sarah Romac
Science, 2015, 348 (6237), pp.1261605. ⟨10.1126/science.1261605⟩
Journal articles hal-01253979v1

Environmental characteristics of Agulhas rings affect interocean plankton transport

Emilie Villar , Gregory Farrant , Michael Follows , Laurence Garczarek , Sabrina Speich
Science, 2015, 348 (6237), pp.1261447 - 1261447. ⟨10.1126/science.1261447⟩
Journal articles hal-01893637v1
Image document

Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome

Lise Pingault , Frédéric Choulet , Adriana A. Alberti , Natasha Marie Glover , Patrick Wincker
Genome Biology, 2015, 16 (1), n.p. ⟨10.1186/s13059-015-0601-9⟩
Journal articles hal-02635440v1

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

Christophe Plomion , Jean-Marc Aury , Joëlle Amselem , Tina Alaeitabar , Valérie Barbe
Molecular Ecology Resources, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩
Journal articles hal-01579667v1
Image document

Structure and function of the global ocean microbiome

Shinichi Sunagawa , Luis Pedro Coelho , Samuel Chaffron , Jens Roat Kultima , Karine Labadie
Science, 2015, 348 (6237), pp.1261359. ⟨10.1126/science.1261359⟩
Journal articles hal-01233742v1
Image document

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

Magali Lescot , Pascal Hingamp , Kenji K Kojima , Emilie Villar , Sarah Romac
The International Society of Microbiologial Ecology Journal, 2015, 10 (5), pp.1134-1146. ⟨10.1038/ismej.2015.192⟩
Journal articles hal-01258212v1
Image document

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.

Camille Berthelot , Frédéric Brunet , Domitille Chalopin , Amélie Juanchich , Maria Bernard
Nature Communications, 2014, 5, pp.1-10. ⟨10.1038/ncomms4657⟩
Journal articles hal-01193812v1

Ancient hybridizations among the ancestral genomes of bread wheat

T. Marcussen , S. Sandve , L. Heier , M. Spannagl , M. Pfeifer
Science, 2014, 345 (6194), pp.1250092-1250092. ⟨10.1126/science.1250092⟩
Journal articles hal-02889053v1
Image document

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Ramiro Logares , Shinichi Sunagawa , Guillem Salazar , Francisco M. Cornejo-Castillo , Isabel Ferrera
Environmental Microbiology, 2014, 16 (9, SI), pp.2659-2671. ⟨10.1111/1462-2920.12250⟩
Journal articles hal-01258219v1

Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis in Podospora anserina

Pierre Grognet , Frédérique Bidard , Claire Kuchly , Laetitia Chan Ho Tong , Evelyne Coppin
Genetics, 2014, 197 (1), pp.421-432. ⟨10.1534/genetics.113.159988⟩
Journal articles hal-03153569v1

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Boulos Chalhoub , France Denoeud , Shengyi Liu , Isobel A. P. Parkin , Haibao Tang
Science, 2014, 345 (6199), pp.950-953. ⟨10.1126/science.1253435⟩
Journal articles hal-01208705v1
Image document

Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus

Florian Humily , Gregory K. Farrant , Dominique Marie , Frédéric Partensky , Sophie Mazard
FEMS Microbiology Ecology, 2014, 88 (2), pp.231-249. ⟨10.1111/1574-6941.12285⟩
Journal articles hal-01100993v1
Image document

Structural and Functional Partitioning of Bread Wheat Chromosome 3B

Frédéric Choulet , Adriana A. Alberti , Sébastien Theil , Natasha Marie Glover , Valérie Barbe
Science, 2014, 345 (6194), ⟨10.1126/science.1249721⟩
Journal articles hal-02638189v1
Image document

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

France Denoeud , Lorenzo Carretero-Paulet , Alexis Dereeper , Gaëtan Droc , Romain Guyot
Science, 2014, 345 (6201), pp.1181-1184. ⟨10.1126/science.1255274⟩
Journal articles hal-02641562v1
Image document

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

Adriana A. Alberti , Caroline Belser , Stefan Engelen , Laurie Bertrand , Celine Orvain
BMC Genomics, 2014, 15, pp.912. ⟨10.1186/1471-2164-15-912⟩
Journal articles hal-02503091v1
Image document

Organization and evolution of transposable elements along the bread wheat chromosome 3B

Josquin Daron , Natasha Glover , Lise Pingault , Sébastien Theil , Véronique Jamilloux
Genome Biology, 2014, 15 (12), pp.1-15. ⟨10.1186/s13059-014-0546-4⟩
Journal articles hal-02630315v1
Image document

Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates

Benoit G. Godard , Marion Coolen , Sophie Le Panse , Aurélie Gombault , Susana Ferreiro-Galve
Biology Open, 2014, 3, pp.1098-1107. ⟨10.1242/bio.20148037⟩
Journal articles hal-01087670v1
Image document

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

Betina M Porcel , France Denoeud , Fred Opperdoes , Benjamin Noel ,