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Laboratory

Genomic analysis of eukaryotes

Publications



Published on 8 October 2019
Publications
  
The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
Alsos IG, Lavergne S, Merkel MKF, Boleda M, Lammers Y, Alberti A, Pouchon C, Denoeud F, Pitelkova I, Puscas M, Roquet C, Hurdu BI, Thuiller W, Zimmermann NE, Hollingsworth PM and Coissac E
Plastome comparative genomics in maples resolves the infrageneric backbone relationships
Areces-Berazain F, Wang YX, Hinsinger DD and Strijk JS
Continued Adaptation of C-4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses
Bianconi ME, Hackel J, Vorontsova MS, Alberti A, Arthan W, Burke SV, Duvall MR, Kellogg EA, Lavergne S, McKain MR, Meunier A, Osborne CP, Traiperm P, Christin PA and Besnard G
TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages
Bottai D, Frigui W, Sayes F, Di Luca M, Spadoni D, Pawlik A, Zoppo M, Orgeur M, Khanna V, Hardy D, Mangenot S, Barbe V, Medigue C, Ma L, Bouchier C, Tavanti A, Larrouy-Maumus G and Brosch R
An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities
Brandt MI, Trouche B, Henry N, Liautard-Haag C, Maignien L, de Vargas C, Wincker P, Poulain J, Zeppilli D and Arnaud-Haond S
Large scale patterns of marine diatom richness: Drivers and trends in a changing ocean
Busseni G, Caputi L, Piredda R, Fremont P, Mele BH, Campese L, Scalco E, de Vargas C, Bowler C, d'Ovidio F, Zingone A, d'Alcala MR and Iudicone D
Metagenomic Mining for Amine Dehydrogenase Discovery
Caparco AA, Pelletier E, Petit JL, Jouenne A, Bommarius BR, de Berardinis V, Zaparucha A, Champion JA, Bommarius AS and Vergne-Vaxelaire C
A framework for in situ molecular characterization of coral holobionts using nanopore sequencing
Carradec Q, Poulain J, Boissin E, Hume BCC, Voolstra CR, Ziegler M, Engelen S, Cruaud C, Planes S and Wincker P
Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria
Dore H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, Pitt FD, Ostrowski M, Six C, Brillet-Gueguen L, Hoebeke M, Bisch A, Le Corguille G, Corre E, Labadie K, Aury JM, Wincker P, Choi DH, Noh JH, Eveillard D, Scanlan DJ, Partensky F and Garczarek L
Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions
Endo H, Blanc-Mathieu R, Li YZ, Salazar G, Henry N, Labadie K, de Vargas C, Sullivan MB, Bowler C, Wincker P, Karp-Boss L, Sunagawa S and Ogata H
Tara Pacific Expedition's Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans: Overview and Preliminary Results
Flores JM, Bourdin G, Altaratz O, Trainic M, Lang-Yona N, Dzimban E, Steinau S, Tettich F, Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Douville E, Forcioli D, Furla P, Galand PE, Sullivan MB, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sunagawa S, Thomas OP, Trouble R, de Vargas C, Thurber RV, Voolstra CR, Wincker P, Zoccola D, Bowler C, Gorsky G, Rudich Y, Vardi A and Koren I
Persistence of environmental DNA in cultivated soils: implication of this memory effect for reconstructing the dynamics of land use and cover changes
Foucher A, Evrard O, Ficetola GF, Gielly L, Poulain J, Giguet-Covex C, Laceby JP, Salvador-Blanes S, Cerdan O and Poulenard J
Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2
Freel KC, Fouteau S, Roche D, Farasin J, Huber A, Koechler S, Peres M, Chiboub O, Varet H, Proux C, Deschamps J, Briandet R, Torchet R, Cruveiller S, Lievremont D, Coppee JY, Barbe V and Arsene-Ploetze F
REPLY TO KU AND SUN: Ancestors of modern giant and large eukaryotic dsDNA viruses infected proto-eukaryotes
Guglielmini J, Woo AC, Krupovic M, Forterre P and Gaia M
Biogeography of soil microbial habitats across France
Karimi B, Villerd J, Dequiedt S, Terrat S, Boure NCP, Djemiel C, Lelievre M, Tripied J, Nowak V, Saby NPA, Bispo A, Jolivet C, Arrouays D, Wincker P, Cruaud C and Ranjard L
Investigating population-scale allelic differential expression in wild populations ofOithona similis(Cyclopoida, Claus, 1866)
Laso-Jadart R, Sugier K, Petit E, Labadie K, Peterlongo P, Ambroise C, Wincker P, Jamet JL and Madoui MA
Genome Resolved Biogeography of Mamiellales
Leconte J, Benites LF, Vannier T, Wincker P, Piganeau G and Jaillon O
Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems
Manzano-Marin A, d'acier AC, Clamens AL, Orvain C, Cruaud C, Barbe V and Jousselin E
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
Sato S, Nanjappa D, Dorrell RG, Vieira FRJ, Kazamia E, Tirichine L, Veluchamy A, Heilig R, Aury JM, Jaillon O, Wincker P, Fussy Z, Obornik M, Munoz-Gomez SA, Mann DG, Bowler C and Zingone A
Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability
Sordino P, D'Aniello S, Pelletier E, Wincker P, Nittoli V, Stemmann L, Mazzocchi MG, Lombard F, Iudicone D and Caputi L
Tara Oceans: towards global ocean ecosystems biology
Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C and Tara Oceans C
Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
Vorobev A, Dupouy M, Carradec Q, Delmont TO, Annamale A, Wincker P and Pelletier E
Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea
Arif M, Gauthier J, Sugier K, Iudicone D, Jaillon O, Wincker P, Peterlongo P and Madoui MA
An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity
Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P and Pompanon F
Specialization of small non-conjugative plasmids in Escherichia coli according to their family types
Branger C, Ledda A, Billard-Pomares T, Doublet B, Barbe V, Roche D, Medigue C, Arlet G and Denamur E
Meta-Omics Reveals Genetic Flexibility of Diatom Nitrogen Transporters in Response to Environmental Changes
Busseni G, Vieira FRJ, Amato A, Pelletier E, Karlusich JJP, Ferrante MI, Wincker P, Rogato A, Bowler C, Sanges R, Maiorano L, Chiurazzi M, d'Alcala MR, Caputi L and Iudicone D
Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems
Caputi L, Carradec Q, Eveillard D, Kirilovsky A, Pelletier E, Karlusich JJP, Vieira FRJ, Villar E, Chaffron S, Malviya S, Scalco E, Acinas SG, Alberti A, Aury JM, Benoiston AS, Bertrand A, Biard T, Bittner L, Boccara M, Brum JR, Brunet C, Busseni G, Carratala A, Claustre H, Coelho LP, Colin S, D'Aniello S, Da Silva C, Del Core M, Dore H, Gasparini S, Kokoszka F, Jamet JL, Lejeusne C, Lepoivre C, Lescot M, Lima-Mendez G, Lombard F, Lukes J, Maillet N, Madoui MA, Martinez E, Mazzocchi MG, Neou MB, Paz-Yepes J, Poulain J, Ramondenc S, Romagnan JB, Roux S, Manta DS, Sanges R, Speich S, Sprovieri M, Sunagawa S, Taillandier V, Tanaka A, Tirichine L, Trottier C, Uitz J, Veluchamy A, Vesela J, Vincent F, Yau S, Kandels-Lewis S, Searson S, Dimier C, Picheral M, Bork P, Boss E, De Vargas C, Follows MJ, Grimsley N, Guidi L, Hingamp P, Karsenti E, Sordino P, Stemmann L, Sullivan MB, Tagliabue A, Zingone A, Garczarek L, d'Ortenzio F, Testor P, Not F, d'Alcala MR, Wincker P, Bowler C, Iudicone D, Gorsky G, Jaillon O, Karp-Boss L, Krzic U, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Velayoudon D, Weissenbach J and Tara Oceans C
Assessing the viral content of uncultured picoeukaryotes in the global-ocean by single cell genomics
Castillo YM, Mangot JF, Benites LF, Logares R, Kuronishi M, Ogata H, Jaillon O, Massana R, Sebastian M and Vaque D
Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica
de Carvalho JF, Lucas J, Deniot G, Falentin C, Filangi O, Gilet M, Legeai F, Lode M, Morice J, Trotoux G, Aury JM, Barbe V, Keller J, Snowdon R, He ZS, Denoeud F, Wincker P, Bancroft I, Chevre AM and Rousseau-Gueutin M
Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.)
Gali KK, Tar'an B, Madoui MA, van der Vossen E, van Oeveren J, Labadie K, Berges H, Bendahmane A, Lachagari RVB, Burstin J and Warkentin T
Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016-2018)
Gorsky G, Bourdin G, Lombard F, Pedrotti ML, Audrain S, Bin N, Boss E, Bowler C, Cassar N, Caudan L, Chabot G, Cohen NR, Cron D, De Vargas C, Dolan JR, Douville E, Elineau A, Flores JM, Ghiglione JF, Haentjens N, Hertau M, John SG, Kelly RL, Koren I, Lin YJ, Marie D, Moulin C, Moucherie Y, Pesant S, Picheral M, Poulain J, Pujo-Pay M, Reverdin G, Romac S, Sullivan MB, Trainic M, Tressol M, Trouble R, Vardi A, Voolstra CR, Wincker P, Agostini S, Banaigs B, Boissin E, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Thomas OP, Thurber RLV, Zoccola D, Planes S, Allemand D, Karsenti E, Banaig B, Iwankow G, Beraud E, Djerbi N, McMind R, Ottaviani A, Rottinger E, Rouan A, Zamoum T, Flume BCC, Pogoreutz C, Rothig T, Ziegler M, Paoli L, Ruscheweyh HJ, Salazar G, Lang-Yona N, Conan P, Hochart C, Bourgois E, Lancelot J, Monmarche D, Karp-Boss L, Mitsuhashi G, Kitano Y, da Silva O, Lemee R, Cronin D, Sullivan M, Armstrong E, Aury JM, Barbe V, Belser C, Carradec Q, Labadie K, Le-Hoang J, Noel B, Klinges G, Vega-Thunder R, Bonnival E, Henry N, Miguel-Gorda M, Friedrich R, Lin Y, Filee J and Tara Pacific C
Marine DNA Viral Macro- and Microdiversity from Pole to Pole
Gregory AC, Zayed AA, Conceicao-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Dominguez-Huerta G, Ferland J, Kandels S, Liu YX, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JE, Vik D, Babin M, Bowler C, Culley AI, De Vargas C, Dutilh BE, Ludicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB and Tara Oceans C
Global Trends in Marine Plankton Diversity across Kingdoms of Life
Ibarbalz FM, Henry N, Brandao MC, Martini V, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahe F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Saez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, de Vargas C, Follows M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Iudicone D, Jaillon O, Karp-Boss L, Karsenti E, Not F, Ogata H, Poulton N, Raes J, Sardet C, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Bopp L, Lombard F, Zinger L and Tara Oceans C
"Microbial Ecotoxicology of Marine Plastic Debris: A Review on Colonization and Biodegradation by the ""Plastisphere"""
Jacquin J, Cheng JG, Odobel C, Pandin C, Conan P, Pujo-Pay M, Barbe V, Meistertzheim AL and Ghiglione JF
An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome
John U, Lu YM, Wohlrab S, Groth M, Janouskovec J, Kohli GS, Mark FC, Bickmeyer U, Farhat S, Felder M, Frickenhaus S, Guillou L, Keeling PJ, Moustafa A, Porcel BM, Valentin K and Glockner G
Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity
Karimi B, Dequiedt S, Terrat S, Jolivet C, Arrouays D, Wincker P, Cruaud C, Bispo A, Prevost-Boure NC and Ranjard L
A reference genome for pea provides insight into legume genome evolution
Kreplak J, Madoui MA, Capal P, Novak P, Labadie K, Aubert G, Bayer PE, Gali KK, Syme RA, Main D, Klein A, Berard A, Vrbova I, Fournier C, d'Agata L, Belser C, Berrabah W, Toegelova H, Milec Z, Vrana J, Lee H, Kougbeadjo A, Terezol M, Huneau C, Turo CJ, Mohellibi N, Neumann P, Falque M, Gallardo K, McGee R, Tar'an B, Bendahmane A, Aury JM, Batley J, Le Paslier MC, Ellis N, Warkentin TD, Coyne CJ, Salse J, Edwards D, Lichtenzveig J, Macas J, Dolezel J, Wincker P and Burstin J
The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle
Leclere L, Horin C, Chevalier S, Lapebie P, Dru P, Peron S, Jager M, Condamine T, Pottin K, Romano S, Steger J, Sinigaglia C, Barreau C, Artigas GQ, Ruggiero A, Fourrage C, Kraus JEM, Poulain J, Aury JM, Wincker P, Queinnec E, Technau U, Manuel M, Momose T, Houliston E and Copley RR
Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist
Monteil CL, Vallenet D, Menguy N, Benzerara K, Barbe V, Fouteau S, Cruaud C, Floriani M, Viollier E, Adryanczyk G, Leonhardt N, Faivre D, Pignol D, Lopez-Garcia P, Weld RJ and Lefevre CT
Elucidation of Codon Usage Signatures across the Domains of Life
Novoa EM, Jungreis I, Jaillon O and Kellis M
Phylogenomics using low-depth whole genome sequencing: A case study with the olive tribe
Olofsson JK, Cantera I, Van de Paer C, Hong-Wa C, Zedane L, Dunning LT, Alberti A, Christin PA and Besnard G
"The Tara Pacific expedition-A pan-ecosystemic approach of the ""-omics"" complexity of coral reef holobionts across the Pacific Ocean"
Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Bourdin G, Bowler C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Ghiglione JF, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sullivan MB, Sunagawa S, Thomas OP, Trouble R, de Vargas C, Thurber RV, Voolstra CR, Wincker P, Zoccola D, Armstrong E, Audrain S, Aury JM, Banaig B, Barbe V, Belser C, Beraud E, Bonnival E, Bourgois E, Carradec Q, Cassar N, Cohen NR, Conan P, Cronin DR, da Silva O, Djerbi N, Dolan JR, Herta GD, Du J, Filee J, Friedrich R, Gorsky G, Guinther M, Haentjens N, Henry N, Hertau M, Hochart C, Hume BCC, Iwankow G, John SG, Karp-Boss L, Kelly RL, Kitano Y, Klinges G, Koren I, Labadie K, Lancelot J, Lang-Yona N, Le-Hoang J, Lemee R, Lin Y, Marie D, McMind R, Miguel-Gordo M, Trainic M, Monmarche D, Mucherie Y, Noel B, Ottaviani A, Paoli L, Pedrotti ML, Pogoreutz C, Pujo-Pay M, Reverdin G, Rothig T, Rottinger E, Rouan A, Ruscheweyh HJ, Salazar G, Vardi A, Vega-Thunder R, Zahed A, Zamoum T, Ziegler M and Tara Pacific C
Transposition favors the generation of large effect mutations that may facilitate rapid adaption
Quadrana L, Etcheverry M, Gilly A, Caillieux E, Madoui MA, Guy J, Silveira AB, Engelen S, Baillet V, Wincker P, Aury JM and Colot V
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sanchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, de Vargas C, Follows M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Not F, Ogata H, Pesant S, Poulton N, Raes J, Sardet C, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Wincker P and Tara Oceans C
Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
Sieracki ME, Poulton NJ, Jaillon O, Wincker P, de Vargas C, Rubinat-Ripoll L, Stepanauskas R, Logares R and Massana R
A gene graveyard in the genome of the fungus Podospora comata
Silar P, Dauget JM, Gautier V, Grognet P, Chablat M, Hermann-Le Denmat S, Couloux A, Wincker P and Debuchy R
A thousand plants' phylogeny
Wincker P
Metagenomic Analysis of Cyanobacteria in an Oligotrophic Tropical Estuary, South Atlantic
Affe HMD, Rigonato J, Nunes JMD and Menezes M
Convergent genomic signatures of domestication in sheep and goats
Alberto FJ, Boyer F, Orozco-terWengel P, Streeter I, Servin B, de Villemereuil P, Benjelloun B, Librado P, Biscarini F, Colli L, Barbato M, Zamani W, Alberti A, Engelen S, Stella A, Joost S, Ajmone-Marsan P, Negrini R, Orlando L, Rezaei HR, Naderi S, Clarke L, Flicek P, Wincker P, Coissac E, Kijas J, Tosser-Klopp G, Chikhi A, Bruford MW, Taberlet P and Pompanon F
Shifting the limits in wheat research and breeding using a fully annotated reference genome
Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N, Pozniak CJ, Choulet F, Distelfeld A, Poland J, Ronen G, Sharpe AG, Pozniak C, Barad O, Baruch K, Keeble-Gagnere G, Mascher M, Ben-Zvi G, Josselin AA, Himmelbach A, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Koh C, Muehlbauer G, Pasam RK, Paux E, Rigault P, Tibbits J, Tiwari V, Spannagl M, Lang D, Gundlach H, Haberer G, Mayer KFX, Ormanbekova D, Prade V, Simkova H, Wicker T, Swarbreck D, Rimbert H, Felder M, Guilhot N, Kaithakottil G, Keilwagen J, Leroy P, Lux T, Twardziok S, Venturini L, Juhasz A, Abrouk M, Fischer I, Uauy C, Borrill P, Ramirez-Gonzalez RH, Arnaud D, Chalabi S, Chalhoub B, Cory A, Datla R, Davey MW, Jacobs J, Robinson SJ, Steuernagel B, van Ex F, Wulff BBH, Benhamed M, Bendahmane A, Concia L, Latrasse D, Alaux M, Bartos J, Bellec A, Berges H, Dolezel J, Frenkel Z, Gill B, Korol A, Letellier T, Olsen OA, Singh K, Valarik M, van der Vossen E, Vautrin S, Weining S, Fahima T, Glikson V, Raats D, Cihalikova J, Toegelova H, Vrana J, Sourdille P, Darrier B, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Jones JDG, Witek K, Yu GT, Small I, Melonek J, Zhou RN, Belova T, Kanyuka K, King R, Nilsen K, Walkowiak S, Cuthbert R, Knox R, Wiebe K, Xiang DQ, Rohde A, Golds T, Cizkova J, Akpinar BA, Biyiklioglu S, Gao LL, N'Daiye A, Kubalakova M, Safar J, Alfama F, Adam-Blondon AF, Flores R, Guerche C, Loaec M, Quesneville H, Condie J, Ens J, Maclachlan R, Tan YF, Alberti A, Aury JM, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Kaur G, Luo MC, Sehgal S, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS, Holusova K, Plihal O, Clark MD, Heavens D, Kettleborough G, Wright J, Balcarkova B, Hu YQ, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu JZ, Cattonaro F, Jiumeng M, Kugler K, Pfeifer M, Sandve S, Xun X, Zhan BJ, Batley J, Bayer PE, Edwards D, Hayashi S, Tulpova Z, Visendi P, Song WN, Cui LC, Du XH, Feng KW, Nie XJ, Tong W, Wang L, Iwgsc, Principal IR, Prin IW-GA, Whole-genome Sequencing A, Hi CD-bS, Whole-genome Assembly Q, Pseudomolecule A, RefSeq Genome Structure G, Automated A, Manual Gene C, Subgenome Comparative A, Transposable E, Phylogenomic A, Transcriptome Anal RNAsD, Whole-genome M, Histone Mark A, W BACCMI-B, Chromosome LTCMPM, Mapping RH, Optical M, Recombination A, Gene Family A, Family CBFG, Dehydrin Gene F, Family NLRG, Family PPRG, Prolamin Gene F, Family WAKG, Stem Solidness SQTLT, Flowering Iocus CFLCGT, Genome Size A, Micro RNAtA, Genetic Maps M, Sorting BACLC, Repository BACPBL, Repository ISD, Phys Maps BACbSA, Assembly BBS, Mapping DDDP, Mapping ALP, Mapping ASP, Wh BDBBDIB, BAC DSPM, Assembly DBS, Ass APMBS, Assembly BBS, Sequencing APMB, Sequencing BPMB, Assembly DBS, Sequencing DLPMB, Figures and Manuscript Writing T
Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family
Bastard K, Isabet T, Stura EA, Legrand P and Zaparucha A
Scientific Reports 8 (), e16587, 2018
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps
Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chevre AM, Delourme R, Deniot G, Denoeud F, Duffe P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M, Barbe V, Cruaud C, Wincker P and Aury JM
A global ocean atlas of eukaryotic genes
Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Meheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C and Wincker P
The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes
Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie K, Cruaud C, Engelen S, Scarcelli N, Rhone B, Burgarella C, Dupuy C, Larmande P, Wincker P, Francois O, Sabot F and Vigouroux Y
Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean
Decelle J, Carradec Q, Pochon X, Henry N, Romac S, Mahe F, Dunthorn M, Kourlaiev A, Voolstra CR, Wincker P and de Vargas C
De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
Dutreux F, Da Silva C, d'Agata L, Couloux A, Gay EJ, Istace B, Lapalu N, Lemainque A, Linglin J, Noel B, Wincker P, Cruaud C, Rouxel T, Balesdent MH and Aury JM
Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Amoebophrya Strains
Farhat S, Florent I, Noel B, Kayal E, Da Silva C, Bigeard E, Alberti A, Labadie K, Corre E, Aury JM, Rombauts S, Wincker P, Guillou L and Porcel BM
Neobodonids are dominant kinetoplastids in the global ocean
Flegontova O, Flegontov P, Malviya S, Poulain J, de Vargas C, Bowler C, Lukes J and Horak A
Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation
Gaulin E, Pel MJC, Camborde L, San-Clemente H, Courbier S, Dupouy MA, Lengelle J, Veyssiere M, Le Ru A, Grandjean F, Cordaux R, Moumen B, Gilbert C, Cano LM, Aury JM, Guy J, Wincker P, Bouchez O, Klopp C and Dumas B
Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria
Grebert T, Dore H, Partensky F, Farrant GK, Boss ES, Picheral M, Guidi L, Pesant S, Scanlan DJ, Wincker P, Acinas SG, Kehoe DM and Garczarek L
An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region
Hume BCC, Ziegler M, Poulain J, Pochon X, Romac S, Boissin E, De Vargas C, Planes S, Wincker P and Voolstra CR
Disentangling the Causes for Faster-X Evolution in Aphids
Jaquiery J, Peccoud J, Ouisse T, Legeai F, Prunier-Leterme N, Gouin A, Nouhaud P, Brisson JA, Bickel R, Purandare S, Poulain J, Battail C, Lemaitre C, Mieuzet L, Le Trionnaire G, Simon JC and Rispe C
Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export
Leblanc K, Queguiner B, Diaz F, Cornet V, Michel-Rodriguez M, de Madron XD, Bowler C, Malviya S, Thyssen M, Gregori G, Rembauville M, Grosso O, Poulain J, de Vargas C, Pujo-Pay M and Conan P
Amphioxus functional genomics and the origins of vertebrate gene regulation
Marletaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutierrez E, Canestro C, Castro F, D'Aniello S, Ferrier DEK, Huang SF, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu AL, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernandez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gomez-Skarmeta JL and Irimia M
Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network
Meng A, Corre E, Probert I, Gutierrez-Rodriguez A, Siano R, Annamale A, Alberti A, Da Silva C, Wincker P, Le Crom S, Not F and Bittner L
A de novo approach to disentangle partner identity and function in holobiont systems
Meng A, Marchet C, Corre E, Peterlongo P, Alberti A, Da Silva C, Wincker P, Pelletier E, Probert I, Decelle J, Le Crom S, Not F and Bittner L
Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages
Morard R, Garet-Delmas MJ, Mahe F, Romac S, Poulain J, Kucera M and de Vargas C
Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle
Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsan K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, Zifcakova L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury JM, Wincker P, Grigoriev IV, Bonfante P and Martin FM
Genome evolution across 1,011 Saccharomyces cerevisiae isolates
Peter J, De Chiara M, Friedrich A, Yue JX, Pflieger D, Bergstrom A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G and Schacherer J
The Rosa genome provides new insights into the domestication of modern roses
Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C, Carrere S, Caissard JC, Couloux A, Cottret L, Aury JM, Szecsi J, Latrasse D, Madoui MA, Francois L, Fu XP, Yang SH, Dubois A, Piola F, Larrieu A, Perez M, Labadie K, Perrier L, Govetto B, Labrousse Y, Villand P, Bardoux C, Boltz V, Lopez-Roques C, Heitzler P, Vernoux T, Vandenbussche M, Quesneville H, Boualem A, Bendahmane A, Liu C, Le Bris M, Salse J, Baudino S, Benhamed M, Wincker P and Bendahmane M
Gene flow contributes to diversification of the major fungal pathogen Candida albicans
Ropars J, Maufrais C, Diogo D, Marcet-Houben M, Perin A, Sertour N, Mosca K, Permal E, Laval G, Bouchier C, Ma L, Schwartz K, Voelz K, May RC, Poulain J, Battail C, Wincker P, Borman AM, Chowdhary A, Fan S, Kim SH, Le Pape P, Romeo O, Shin JH, Gabaldon T, Sherlock G, Bougnoux ME and d'Enfert C
Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans
Seeleuthner Y, Mondy S, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, de Vargas C, Wincker P and Tara Oceans C
Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy
Sugier K, Vacherie B, Cornils A, Wincker P, Jamet JL and Madoui MA
The Ocean Gene Atlas: exploring the biogeography of plankton genes online
Villar E, Vannier T, Vernette C, Lescot M, Cuenca M, Alexandre A, Bachelerie P, Rosnet T, Pelletier E, Sunagawa S and Hingamp P
Nucleic Acids Research 46 (W1), W289-W295, 2018
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
Ziegler M, Quere G, Ghiglione JF, Iwankow G, Barbe V, Boissin E, Wincker P, Planes S and Voolstra CR
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition
Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernandez-Gomez B, Bowler C, Cochrane G, Amid C, Ten Hoopen P, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Pesant S, Karsenti E, Wincker P, Genoscope Tech T and Tara Oceans C
A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications
Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, Jaillon O, Not F, Nunes F, Payri C, Wincker P and Barbe V
Towards standards for human fecal sample processing in metagenomic studies
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, Vlieg JVH, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao LP, Zoetendal EG, Ehrlich SD, Dore J and Bork P
Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges
Gouin A, Bretaudeau A, Nam K, Gimenez S, Aury JM, Duvic B, Hilliou F, Durand N, Montagne N, Darboux I, Kuwar S, Chertemps T, Siaussat D, Bretschneider A, Mone Y, Ahn SJ, Hanniger S, Grenet ASG, Neunemann D, Maumus F, Luyten I, Labadie K, Xu W, Koutroumpa F, Escoubas JM, Llopis A, Maibeche-Coisne M, Salasc F, Tomar A, Anderson AR, Khan SA, Dumas P, Orsucci M, Guy J, Belser C, Alberti A, Noel B, Couloux A, Mercier J, Nidelet S, Dubois E, Liu NY, Boulogne I, Mirabeau O, Le Goff G, Gordon K, Oakeshott J, Consoli FL, Volkoff AN, Fescemyer HW, Marden JH, Luthe DS, Herrero S, Heckel DG, Wincker P, Kergoat GJ, Amselem J, Quesneville H, Groot AT, Jacquin-Joly E, Negre N, Lemaitre C, Legeai F, d'Alencon E and Fournier P
de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C, Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J and Aury JM
New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona
Madoui MA, Poulain J, Sugier K, Wessner M, Noel B, Berline L, Labadie K, Cornils A, Blanco-Bercial L, Stemmann L, Jamet JL and Wincker P
Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells
Mangot JF, Logares R, Sanchez P, Latorre F, Seeleuthner Y, Mondy S, Sieracki ME, Jaillon O, Wincker P, de Vargas C and Massana R
Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination
Sun S, Yadav V, Billmyre RB, Cuomo CA, Nowrousian M, Wang LY, Souciet JL, Boekhout T, Porcel B, Wincker P, Granek JA, Sanyal K and Heitman J
A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications
Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, Jaillon O, Not F, Nunes F, Payri C, Wincker P and Barbe V
Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton
Cornejo-Castillo FM, Cabello AM, Salazar G, Sanchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R and Acinas SG
Plankton networks driving carbon export in the oligotrophic ocean
Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum JR, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G and Tara Oceans Consortium C
Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages
Lescot M, Hingamp P, Kojima KK, Villar E, Romac S, Veluchamy A, Boccara M, Jaillon O, Iudicone D, Bowler C, Wincker P, Claverie JM and Ogata H
Insights into global diatom distribution and diversity in the world's ocean
Malviya S, Scalco E, Audic S, Vincenta F, Veluchamy A, Poulain J, Wincker P, Iudicone D, de Vargas C, Bittner L, Zingone A and Bowler C
Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies
Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Berges H, Bodenes C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leple JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H and Kremer A
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D, Bork P, Acinas SG, Wincker P, Sullivan MB and Tara Oceans C
Survey of the green picoalga Bathycoccus genomes in the global ocean
Vannier T, Leconte J, Seeleuthner Y, Mondy S, Pelletier E, Aury JM, de Vargas C, Sieracki M, Iudicone D, Vaulot D, Wincker P and Jaillon O
Non-invasive prenatal testing for trisomy 21 based on analysis of cell-free fetal DNA circulating in the maternal plasma
Alberti A, Salomon LJ, Le Lorc'h M, Couloux A, Bussieres L, Goupil S, Malan V, Pelletier E, Hyon C, Vialard F, Rozenberg P, Bouhanna P, Oury JF, Schmitz T, Romana S, Weissenbach J, Vekemans M and Ville Y
Patterns and ecological drivers of ocean viral communities
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB and Tara Oceans C
Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides
Czernic P, Gully D, Cartieaux F, Moulin L, Guefrachi I, Patrel D, Pierre O, Fardoux J, Chaintreuil C, Nguyen P, Gressent F, Da Silva C, Poulain J, Wincker P, Rofidal V, Hem S, Barriere Q, Arrighi JF, Mergaert P and Giraud E
Eukaryotic plankton diversity in the sunlit ocean
de Vargas C, Audic S, Henry N, Decelle J, Mahe F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horak A, Jaillon O, Lima-Mendez G, Lukes J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E and Tara Oceans C
Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics
Delmont TO, Eren AM, Maccario L, Prestat E, Esen O, Pelletier E, LePaslier D, Simonet P and Vogel TM
Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi
Fontanillas E, Hood ME, Badouin H, Petit E, Barbe V, Gouzy J, de Vienne DM, Aguileta G, Poulain J, Wincker P, Chen ZH, Toh SS, Cuomo CA, Perlin MH, Gladieux P and Giraud T
Towards the Rose Genome Sequence and Its Use in Research and Breeding
Foucher F, Hibrand-Saint Oyant L, Hamama L, Sakr S, Nybom H, Baudino S, Caissard JP, Hokanson SC, Byrne DM, Smulder JMS, Desnoye B, Debener T, Bruneau A, De Riek J, Matsumoto S, Torres A, Millan T, Amaya I, Yamada K, Wincker P, Zamir D, Gouzy J, Sargent D, Bendahmane M, Raymond O, Vergne P, Dubois A and Just J
Article 1064 (), 167-175, 2015
Determinants of community structure in the global plankton interactome
Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sanchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J and Tara Oceans C
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