| Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences | | Akita S, Vieira C, Hanyuda T, Rousseau F, Cruaud C, Couloux A, Heesch S, Cock JM and Kawai H |  | | Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding | | Aury JM, Engelen S, Istace B, Monat C, Lasserre-Zuber P, Belser C, Cruaud C, Rimbert H, Leroy P, Arribat S, Dufau I, Bellec A, Grimbichler D, Papon N, Paux E, Ranoux M, Alberti A, Wincker P and Choulet F | | | Epigenomic and structural events preclude recombination in Brassica napus | | Boideau F, Richard G, Coriton O, Huteau V, Belser C, Deniot G, Eber F, Falentin C, de Carvalho JF, Gilet M, Lode-Taburel M, Maillet L, Morice J, Trotoux G, Aury JM, Chevre AM and Rousseau-Gueutin M | | | Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection | | Canaguier A, Guilbaud R, Denis E, Magdelenat G, Belser C, Istace B, Cruaud C, Wincker P, Le Paslier MC, Faivre-Rampant P and Barbe V | | | Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France | | Clavel B, Lepetz S, Chauvey L, Schiavinato S, Tonasso-Calviere L, Liu XX, Fages A, Khan N, Seguin-Orlando A, Sarkissian CD, Clavel P, Estrada O, Alioglu D, Gaunitz C, Aury JM, Barme M, Bodu P, Olive M, Bignon-Lau O, Castel JC, Boudadi-Maligne M, Boulbes N, Bourgois A, Decanter F, Foucras S, Frere S, Gardeisen A, Jouanin G, Mela C, Morand N, Espinet AN, Perdereau A, Putelat O, Riviere J, Robin O, Salin M, Valenzuela-Lamas S, Vallet C, Yvinec JH, Wincker P and Orlando L | | | A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs | | Mishra B, Ulaszewski B, Meger J, Aury J-M, Bodenes C, Lesur-Kupin I, Pfenninger M, Da Silva C, Gupta DK, Guichoux E, Heer K, Lalanne C, Labadie K, Opgenoorth L, Ploch S, Le Provost G, Salse J, Scotti I, Wotzel S, Plomion C, Burczyk J and Thines M | | | ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications | | Pouchon C, Boyer F, Roquet C, Denoeud F, Chave J, Coissac E, Alsos IG, Lavergne S, PhyloAlps C and PhyloNorway C | | | Transcriptome of the synganglion in the tick Ixodes ricinus and evolution of the cys-loop ligand-gated ion channel family in ticks | | Rispe C, Hervet C, de la Cotte N, Daveu R, Labadie K, Noel B, Aury JM, Thany S, Taillebois E, Cartereau A, Le Mauff A, Charvet CL, Auger C, Courtot E, Neveu C and Plantard O | | | Genome-wide evolutionary response of European oaks during the Anthropocene | | Saleh D, Chen J, Leple JC, Leroy T, Truffaut L, Dencausse B, Lalanne C, Labadie K, Lesur I, Bert D, Lagane F, Morneau F, Aury JM, Plomion C, Lascoux M and Kremer A | | | Genome-wide mapping of individual replication fork velocities using nanopore sequencing | | Theulot B, Lacroix L, Arbona JM, Millot GA, Jean E, Cruaud C, Pellet J, Proux F, Hennion M, Engelen S, Lemainque A, Audit B, Hyrien O and Le Tallec B | | | Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome | | Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo JR, Mohssen M, Tian FN, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB and Tara Oceans C | | | Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads | | | | | Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing | | Belser C, Baurens FC, Noel B, Martin G, Cruaud C, Istace B, Yahiaoui N, Labadie K, Hribova E, Dolezel J, Lemainque A, Wincker P, D'Hont A and Aury JM | | | Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA | | Brandt MI, Pradillon F, Trouche B, Henry N, Liautard-Haag C, Cambon-Bonavita MA, Cueff-Gauchard V, Wincker P, Belser C, Poulain J, Arnaud-Haond S and Zeppilli D | | | BoardION: real-time monitoring of Oxford Nanopore sequencing instruments | | Bruno A, Aury JM and Engelen S | | | Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids | | Clavel P, Dumoncel J, Sarkissian CD, Seguin-Orlando A, Calviere-Tonasso L, Schiavinato S, Chauvey L, Perdereau A, Aury JM, Wincker P, Onar V, Clavel B, Lepetz S, Braga J and Orlando L | | | Sequence diversity and evolution of a group of iflaviruses associated with ticks | | Daveu R, Hervet C, Sigrist L, Sassera D, Jex A, Labadie K, Aury JM, Plantard O and Rispe C | | | VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity | | Denoyelle L, Talouarn E, Bardou P, Colli L, Alberti A, Danchin C, Del Corvo M, Engelen S, Orvain C, Palhiere I, Rupp R, Sarry J, Salavati M, Amills M, Clark E, Crepaldi P, Faraut T, Masiga CW, Pompanon F, Rosen BD, Stella A, Van Tassell CP, Tosser-Klopp G and VarGoats C | | | Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis | | Dong N, Bandura J, Zhang ZL, Wang Y, Labadie K, Noel B, Davison A, Koene JM, Sun HS, Coutellec MA and Feng ZP | | | Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp | | Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai RB, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouze P, van de Peer Y, Wincker P, Rombauts S, Porcel BM and Guillou L | | | Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes | | Garczarek L, Guyet U, Dore H, Farrant GK, Hoebeke M, Brillet-Gueguen L, Bisch A, Ferrieux M, Siltanen J, Corre E, Le Corguille G, Ratin M, Pitt FD, Ostrowski M, Conan M, Siegel A, Labadie K, Aury JM, Wincker P, Scanlan DJ and Partensky F | | | Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization | | Gauthier J, Boulain H, van Vugt J, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagne N, Boulogne I, Sabeti-Azad M, Maibeche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Consoli FL, Dupas S, Hua-Van A, Le Goff G, Bezier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA and Drezen JM | | | Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant | | Gay EJ, Soyer JL, Lapalu N, Linglin J, Fudal I, Da Silva C, Wincker P, Aury JM, Cruaud C, Levrel A, Lemoine J, Delourme R, Rouxel T and Balesdent MH | | | Population genomics of apricots unravels domestication history and adaptive events | | Groppi A, Liu S, Cornille A, Decroocq S, Bui QT, Tricon D, Cruaud C, Arribat S, Belser C, Marande W, Salse J, Huneau C, Rodde N, Rhalloussi W, Cauet S, Istace B, Denis E, Carrere S, Audergon JM, Roch G, Lambert P, Zhebentyayeva T, Liu WS, Bouchez O, Lopez-Roques C, Serre RF, Debuchy R, Tran J, Wincker P, Chen XL, Petriacq P, Barre A, Nikolski M, Aury JM, Abbott AG, Giraud T and Decroocq V | | | Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case | | Istace B, Belser C, Falentin C, Labadie K, Boideau F, Deniot G, Maillet L, Cruaud C, Bertrand L, Chevre AM, Wincker P, Rousseau-Gueutin M and Aury JM | | | Historical management of equine resources in France from the Iron Age to the Modern Period | | Lepetz S, Clavel B, Alioglu D, Chauvey L, Schiavinato S, Tonasso-Calviere L, Liu XX, Fages A, Khan N, Seguin-Orlando A, Sarkissian CD, Clavel P, Estrada O, Gaunitz C, Aury JM, Barme M, Boulbes N, Bourgois A, Decanter F, Foucras S, Frere S, Gardeisen A, Jouanin G, Mela C, Morand N, Espinet AN, Perdereau A, Putelat O, Riviere J, Robin O, Salin M, Valenzuela-Lamas S, Vallet C, Yvinec JH, Wincker P and Orlando L | | | The origins and spread of domestic horses from the Western Eurasian steppes | | Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calviere L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Sarkissian CD, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregely T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpre M, Hoyo MMD, Wilczynski J, Pospula S, Lasota-Kus A, Tunia K, Nowak M, Rannamae E, Saarma U, Boeskorov G, Lougas L, Kysely R, Peske L, Balasescu A, Dumitrascu V, Dobrescu R, Gerber D, Kiss V, Szecsenyi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsar G, Gal E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Lamas SV, Canadell SA, Espinet AN, Iborra MP, Garrido JL, Gonzalez ER, Celestino S, Olaria C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Gianni GB, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muniz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A and Orlando L | | | Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii | | Reynes L, Thibaut T, Mauger S, Blanfune A, Holon F, Cruaud C, Couloux A, Valero M and Aurelle D | | | Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes | | Sellis D, Guerin F, Arnaiz O, Pett W, Lerat E, Boggetto N, Krenek S, Berendonk T, Couloux A, Aury JM, Labadie K, Malinsky S, Bhullar S, Meyer E, Sperling L, Duret L and Duharcourt S | | | Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing | | Studer F, Petit JL, Engelen S and Mendoza-Parra MA | | | Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient | | Trouche B, Brandt MI, Belser C, Orejas C, Pesant S, Poulain J, Wincker P, Auguet JC, Arnaud-Haond S and Maignien L | | | Complete Genome Sequences of Two Pseudomonas Species Isolated from Marine Environments of the Pacific Ocean | | Wang SZ, Cruaud C, Aury JM, Vallenet D, Poulain J, Vacherie B, Zaparucha A and Vergne-Vaxelaire C | | | Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa | | Boutte J, Maillet L, Chaussepied T, Letort S, Aury JM, Belser C, Boideau F, Brunet A, Coriton O, Deniot G, Falentin C, Huteau V, Lode-Taburel M, Morice J, Trotoux G, Chevre AM, Rousseau-Gueutin M and de Carvalho JF | | | 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 | | | FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing | | Hennion M, Arbona JM, Lacroix L, Cruaud C, Theulot B, Le Tallec B, Proux F, Wu X, Novikova E, Engelen S, Lemainque A, Audit B and Hyrien O | | | BiSCoT: improving large eukaryotic genome assemblies with optical maps | | Istace B, Belser C and Aury JM | | | Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection | | Kayal E, Alves-de-Souza C, Farhat S, Velo-Suarez L, Monjol J, Szymczak J, Bigeard E, Marie D, Noel B, Porcel BM, Corre E, Six C and Guillou L | | | Adaptive introgression as a driver of local adaptation to climate in European white oaks | | Leroy T, Louvet JM, Lalanne C, Le Provost G, Labadie K, Aury JM, Delzon S, Plomion C and Kremer A | | | Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers | | Leroy T, Rougemont Q, Dupouey JL, Bodenes C, Lalanne C, Belser C, Labadie K, Le Provost G, Aury JM, Kremer A and Plomion C | | | Analyses of the Root-Knot Nematode (Meloidogyne graminicola) Transcriptome during Host Infection Highlight Specific Gene Expression Profiling in Resistant Rice Plants | | Petitot AS, Dereeper A, Da Silva C, Guy J and Fernandez D | | | Long-read assembly of the Brassica napus reference genome Darmor-bzh | | Rousseau-Gueutin M, Belser C, Da Silva C, Richard G, Istace B, Cruaud C, Falentin C, Boideau F, Boutte J, Delourme R, Deniot G, Engelen S, de Carvalho JF, Lemainque A, Maillet L, Morice J, Wincker P, Denoeud F, Chevre AM and Aury JM | | | 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 | | | Virus-host coexistence in phytoplankton through the genomic lens | | Yau S, Krasovec M, Benites LF, Rombauts S, Groussin M, Vancaester E, Aury JM, Derelle E, Desdevises Y, Escande ML, Grimsley N, Guy J, Moreau H, Sanchez-Brosseau S, van de Peer Y, Vandepoele K, Gourbiere S and Piganeau G | | | 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 | | | 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 | | | 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 | | | Two large reciprocal translocations characterized in the disease resistance-rich burmannica genetic group of Musa acuminata | | Dupouy M, Baurens FC, Derouault P, Hervouet C, Cardi C, Cruaud C, Istace B, Labadie K, Guiougou C, Toubi L, Salmon F, Mournet P, Rouard M, Yahiaoui N, Lemainque A, Martin G and D'Hont A | | | 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 | | | Complete Genome Sequence of Bradyrhizobium sp. Strain ORS3257, an Efficient Nitrogen-Fixing Bacterium Isolated from Cowpea in Senegal | | Le Quere A, Gully D, Teulet A, Navarro E, Gargani D, Fardoux J, Cruveiller S, Neyra M, Giraud E and Krasova Wade T | | | De novo clustering of long reads by gene from transcriptomics data | | Marchet C, Lecompte L, Da Silva C, Cruaud C, Aury JM, Nicolas J and Peterlongo P | | | Draft Genome Sequence of Tubulinosema ratisbonensis, a Microsporidian Species Infecting the Model Organism Drosophila melanogaster | | Polonais V, Niehus S, Wawrzyniak I, Franchet A, Gaspin C, Belkorchia A, Reichstadt M, Belser C, Labadie K, Couloux A, Delbac F, Peyretaillade E and Ferrandon D | | | 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 | | | Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules | | Sessegolo C, Cruaud C, Da Silva C, Cologne A, Dubarry M, Derrien T, Lacroix V and Aury JM | | | 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 | | | 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 | | | Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland | | Belkhelfa S, Labadie K, Cruaud C, Aury J-M, Roche D, Bouzon M, Salanoubat M and Doring V | | | 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 | | | 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 | | | Phylogeny and salt-tolerance of freshwater Nostocales strains: Contribution to their systematics and evolution | | Duval C, Thomazeau S, Drelin Y, Yepremian C, Bouvy M, Couloux A, Troussellier M, Rousseau F and Bernard C | | | 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 | | | 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 | | | Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication | | Legras JL, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T, Sanchez I, Couloux A, Guy J, Franco-Duarte R, Marcet-Houben M, Gabaldon T, Schuller D, Sampaio JP and Dequin S | | | 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 | | | 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 | | | Oak genome reveals facets of long lifespan | | Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholome J, Faivre-Rampant P, Kohler A, Leple JC, Chantret N, Chen J, Dievart A, Alaeitabar T, Barbe V, Belser C, Berges H, Bodenes C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rue O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A and Salse 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 | | | Hardwood Tree Genomics: Unlocking Woody Plant Biology | | Tuskan GA, Groover AT, Schmutz J, DiFazio SP, Myburg A, Grattapaglia D, Smart LB, Yin TM, Aury JM, Kremer A, Leroy T, Le Provost G, Plomion C, Carlson JE, Randall J, Westbrook J, Grimwood J, Muchero W, Jacobson D and Michener JK | | | 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 | | | The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies | | Argout X, Martin G, Droc G, Fouet O, Labadie K, Rivals E, Aury JM and Lanaud C | | | Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes | | Blanc-Mathieu R, Perfus-Barbeoch L, Aury JM, Da Rocha M, Gouzy J, Sallet E, Martin-Jimenez C, Bailly-Bechet M, Castagnone-Sereno P, Flot JF, Kozlowski DK, Cazareth J, Couloux A, Da Silva C, Guy J, Kim-Jo YJ, Rancurel C, Schiex T, Abad P, Wincker P and Danchin EGJ | | | Untangling species identity in gastropods with polymorphic shells in the genus Bolma Risso, 1826 (Mollusca, Vetigastropoda) | | Castelin M, Williams ST, Buge B, Maestrati P, Lambourdiere J, Ozawa T, Utge J, Couloux A, Alf A and Samadi S | | | The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes | | Danchin EGJ, Perfus-Barbeoch L, Rancurel C, Thorpe P, Da Rocha M, Bajew S, Neilson R, Sokolova E, Da Silva C, Guy J, Labadie K, Esmenjaud D, Helder J, Jones JT and Eves-van den Akker S | | | High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing | | Fournier T, Gounot JS, Freel K, Cruaud C, Lemainque A, Aury JM, Wincker P, Schacherer J and Friedrich A | | | 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 | | | Extensive recent secondary contacts between four European white oak species | | Leroy T, Roux C, Villate L, Bodenes C, Romiguier J, Paiva JAP, Dossat C, Aury JM, Plomion C and Kremer A | | | De Novo Assemblies of Three Oryza glaberrima Accessions Provide First Insights about Pan-Genome of African Rices | | Monat C, Pera B, Ndjiondjop MN, Sow M, Tranchant-Dubreuil C, Bastianelli L, Ghesquiere A and Sabot F | | | Phylogeny and diversification of the cloud forest Morpho sulkowskyi group (Lepidoptera, Nymphalidae) in the evolving Andes | | Nattier R, Capdevielle-Dulac C, Cassilde C, Couloux A, Cruaud C, Lachaume G, Lamas G, Silvain JF and Blandin P | | | De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing | | Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Mass J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM and Usadel B | | | Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis | | Spirhanzlova P, Dhorne-Pollet S, Fellah JS, Da Silva C, Tlapakova T, Labadie K, Weissenbach J, Poulain J, Jaffredo T, Wincker P, Krylov V and Pollet N | | | A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation | | Acemel RD, Tena JJ, Irastorza-Azcarate I, Marletaz F, Gomez-Marin C, de la Calle-Mustienes E, Bertrand S, Diaz SG, Aldea D, Aury JM, Mangenot S, Holland PWH, Devos DP, Maeso I, Escriva H and Gomez-Skarmeta JL | | | Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans Dsij(T) | | Barbeyron T, Thomas F, Barbe V, Teeling H, Schenowitz C, Dossat C, Goesmann A, Leblanc C, Glockner FO, Czjzek M, Amann R and Michel G | | | Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae) | | Boutte J, de Carvalho JF, Rousseau-Gueutin M, Poulain J, Da Silva C, Wincker P, Ainouche M and Salmon A | | | Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20) | | Falentin H, Deutsch SM, Loux V, Hammani A, Buratti J, Parayre S, Chuat V, Barbe V, Aury JM, Jan G and Le Loir Y | | | Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells | | Kole C, Berdugo N, Da Silva C, Ait-Ali N, Millet-Puel G, Pagan D, Blond F, Poidevin L, Ripp R, Fontaine V, Wincker P, Zack DJ, Sahel JA, Poch O and Leveillard T | | | Implication of the suberin pathway in adaptation to waterlogging and hypertrophied lenticels formation in pedunculate oak (Quercus robur L.) | | Le Provost G, Lesur I, Lalanne C, Da Silva C, Labadie K, Aury JM, Leple JC and Plomion C | | | MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling (TM) Data | | Madoui MA, Dossat C, d'Agata L, van Oeveren J, van der Vossen E and Aury JM | | | "Improvement of the banana ""Musa acuminata"" reference sequence using NGS data and semi-automated bioinformatics methods" | | Martin G, Baurens FC, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Dolezel J, Aury JM, Alberti A, Carreel F and D'Hont A | | | Comparative venomics of Psyttalia lounsburyi and P-concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 beta-glucosidase | | Mathe-Hubert H, Colinet D, Deleury E, Belghazi M, Ravallec M, Poulain J, Dossat C, Poirie M and Gatti JL | | | Dual RNA-seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants | | Petitot AS, Dereeper A, Agbessi M, Da Silva C, Guy J, Ardisson M and Fernandez D | |
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