| 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 | | | | 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 | | | | Metatranscriptomics of cheese microbial communities: Efficiency of RNA extraction from various cheese types and of mRNA enrichment | Carbonne C, Labadie K, Cruaud C, Brun E, Barbe V and Monnet C | | | | 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 | | | | Selection drives convergent gene expression changes during transitions to co-sexuality in haploid sexual systems | Cossard GG, Godfroy O, Nehr Z, Cruaud C, Cock JM, Lipinska AP and Coelho SM | | | | Genomic Instability in Somatic Hybridization between Poncirus and Citrus Species Aiming to Create New Rootstocks | Dambier D, Barantin P, Boulard G, Costantino G, Mournet P, Perdereau A, Morillon R and Ollitrault P | | | | Diversity and ecological footprint of Global Ocean RNA viruses | Dominguez-Huerta G, Zayed AA, Wainaina JM, Guo JR, Tian FN, Pratama AA, Bolduc B, Mohssen M, Zablocki O, Pelletier E, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Coordinators TO, Bowler C, Eveillard D, Guidi L, Karsenti E, Kuhn JH, Ogata H, Wincker P, Culley A, Chaffron S and Sullivan MB | | | | Complete Genome Sequence of Tepidibacter sp. Strain 8C15b, Isolated from Bank Sediments of Haiphong Bay, Vietnam | Fouteau S, Van VB, Rouy Z, Beraud M, Cruaud C, Cayol JL, Chifflet S, Van TC, The TP, Vallenet D, Oliveira PH, Mari X and Pradel N | | | | Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria | Grebert T, Garczarek L, Daubin V, Humily F, Marie D, Ratin M, Devailly A, Farrant GK, Mary I, Mella-Flores D, Tanguy G, Labadie K, Wincker P, Kehoe DM and Partensky F | | | | Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei | Lu YAT, Ruault S, Daguin-Thiebaut C, Castel J, Bierne N, Broquet T, Wincker P, Perdereau A, Arnaud-Haond S, Gagnaire PA, Jollivet D, Hourdez S and Bonhomme F | | | | 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 | | | | 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 | | | | Lifespan prolonging mechanisms and insulin upregulation without fat accumulation in long-lived reproductives of a higher termite | Seite S, Harrison MC, Sillam-Dusses D, Lupoli R, Van Dooren TJM, Robert A, Poissonnier LA, Lemainque A, Renault D, Acket S, Andrieu M, Viscarra J, Sul HS, De Beer ZW, Bornberg-Bauer E and Vasseur-Cognet M | | | | 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 | | | | 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 | | | | 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 | | | | 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 | | | | Comparative genomics reveals new functional insights in uncultured MAST species | Labarre A, Lopez-Escard D, Latorre F, Leonard G, Bucchini F, Obiol A, Cruaud C, Sieracki ME, Jaillon O, Wincker P, Vandepoele K, Logares R and Massana R | | | | Niche adaptation promoted the evolutionary diversification of tiny ocean predators | Latorre F, Deutschmann IM, Labarre A, Obiol A, Krabberod AK, Pelletier E, Sieracki ME, Cruaud C, Jaillon O, Massana R and Logares R | | | | 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 | | | | Bacterial Epigenomics: Coming of Age COMMENT | | | | | Segregation Distortion for Male Parents in High Density Genetic Maps from Reciprocal Crosses between Two Self-Incompatible Cultivars Confirms a Gametophytic System for Self-Incompatibility in Citrus | Ollitrault P, Ahmed D, Costantino G, Evrard JC, Cardi C, Mournet P, Perdereau A and Froelicher Y | | | | Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean | Royo-Llonch M, Sanchez P, Ruiz-Gonzalez C, Salazar G, Pedros-Alio C, Sebastian M, Labadie K, Paoli L, Ibarbalz FM, Zinger L, Churcheward B, Chaffron S, Eveillard D, Karsenti E, Sunagawa S, Wincker P, Karp-Boss L, Bowler C, Acinas SG and Tara Oceans C | | | | 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 | | | | Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga | Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Lliros M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot JF and Van Doninck K | | | | Male Differentiation in the Marine Copepod Oithona nana Reveals the Development of a New Nervous Ganglion and Lin12-Notch-Repeat Protein-Associated Proteolysis | Sugier K, Laso-Jadart R, Vacherie B, Kafer J, Bertrand L, Labadie K, Martins N, Orvain C, Petit E, Wincker P, Jamet JL, Alberti A and Madoui MA | | | | 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 | | | | Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench | Zhang WJ, Zhang C, Zhou SY, Li XG, Mangenot S, Fouteau S, Guerin T, Qi XQ, Yang J, Bartlett DH and Wu LF | | | | 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 | | | | Characterization of Mollivirus kamchatka, the First Modern Representative of the Proposed Molliviridae Family of Giant Viruses | Christo-Foroux E, Alempic JM, Lartigue A, Santini S, Labadie K, Legendre M, Abergel C and Claverie JM | | | | 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 | | | | 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 | | | | 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 | | | | 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 | | | | 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 | | | | Chromosome reciprocal translocations have accompanied subspecies evolution in bananas | Martin G, Baurens FC, Hervouet C, Salmon F, Delos JM, Labadie K, Perdereau A, Mournet P, Blois L, Dupouy M, Carreel F, Ricci S, Lemainque A, Yahiaoui N and D'Hont A | | | | Colonization kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant | Morin L, Goubet A, Madigou C, Pernelle JJ, Palmier K, Labadie K, Lemainque A, Michot O, Astoul L, Barbier P, Almayrac JL and Sghir A | | | | The Protector within: Comparative Genomics of APSE Phages across Aphids Reveals Rampant Recombination and Diverse Toxin Arsenals | Rouil J, Jousselin E, d'acier AC, Cruaud C and Manzano-Marin A | | | | 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 | | | | Recombination and Large Structural Variations Shape Interspecific Edible Bananas Genomes | Baurens FC, Martin G, Hervouet C, Salmon F, Yohome D, Ricci S, Rouard M, Habas R, Lemainque A, Yahiaoui N and D'Hont A | | | | Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations | Belkhelfa S, Roche D, Dubois I, Berger A, Delmas VA, Cattolico L, Perret A, Labadie K, Perdereau AC, Darii E, Pateau E, de Berardinis V, Salanoubat M, Bouzon M and Doring V | | | | Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes | Benites LF, Poulton N, Labadie K, Sieracki ME, Grimsleyl N and Piganeau G | | | | 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 | | | | Mixotrophic protists display contrasted biogeographies in the global ocean | Faure E, Not F, Benoiston AS, Labadie K, Bittner L and Ayata SD | | | | 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 | | | | 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 | | | | 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 | | | | 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 | | | | 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 | | | | 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 | | | | The Wolbachia mobilome in Culex pipiens includes a putative plasmid | Reveillaud J, Bordenstein SR, Cruaud C, Shaiber A, Esen OC, Weill M, Makoundou P, Lolans K, Watson AR, Rakotoarivony I and Eren AM | | | | 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 | | | | 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 | | | | 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 | | | | Biogeography of soil bacteria and archaea across France | Karimi B, Terrat S, Dequiedt S, Saby NPA, Horriguel W, Lelievre M, Nowak V, Jolivet C, Arrouays D, Wincker P, Cruaud C, Bispo A, Maron PA, Prevost-Boure NC and Ranjard L | | | | Diversity and evolution of the emerging Pandoraviridae family | Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Coute Y, Abergel C and Claverie JM | | | | A Freeloader? The Highly Eroded Yet Large Genome of the Serratia symbiotica Symbiont of Cinara strobi | Manzano-Marin A, d'acier AC, Clamens AL, Orvain C, Cruaud C, Barbe V and Jousselin E | | | | 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 | | | | 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 | | | | 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 | | | | Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics | Cerisy T, Souterre T, Torres-Romero I, Boutard M, Dubois I, Patrouix J, Labadie K, Berrabah W, Salanoubat M, Doring V and Tolonen AC | | | | 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 | | | | Genetic Architecture of a Rice Nested Association Mapping Population | Fragoso CA, Moreno M, Wang ZH, Heffelfinger C, Arbelaez LJ, Aguirre JA, Franco N, Romero LE, Labadie K, Zhao HY, Dellaporta SL and Lorieux M | | | | Different waves of effector genes with contrasted genomic location are expressed by Leptosphaeria maculans during cotyledon and stem colonization of oilseed rape | Gervais J, Plissonneau C, Linglin J, Meyer M, Labadie K, Cruaud C, Fudal I, Rouxel T and Balesdent MH | | | | 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 | | | | Geography and life history traits account for the accumulation of cryptic diversity among Indo-West Pacific coral reef fishes | Hubert N, Dettai A, Pruvost P, Cruaud C, Kulbicki M, Myers RF and Borsa 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 | | | | Evolution of the Banana Genome (Musa acuminata) Is Impacted by Large Chromosomal Translocations | Martin G, Carreel F, Coriton O, Hervouet C, Cardi C, Derouault P, Roques D, Salmon F, Rouard M, Sardos J, Labadie K, Baurens FC and D'Hont A | | | | Impact of biotic and abiotic factors on the expression of fungal effector-encoding genes in axenic growth conditions | Meyer M, Bourras S, Gervais J, Labadie K, Cruaud C, Balesdent MH and Rouxel T | | | | 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 | | | | 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 | | | | Mapping and predictive variations of soil bacterial richness across France | Terrat S, Horrigue W, Dequietd S, Saby NPA, Lelievre M, Nowak V, Tripied J, Regnier T, Jolivet C, Arrouays D, Wincker P, Cruaud C, Karimi B, Bispo A, Maron PA, Prevost-Boure NC and Ranjard L | | | | Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes | Tran TTT, Mangenot S, Magdelenat G, Payen E, Rouy Z, Belahbib H, Grail BM, Johnson DB, Bonnefoy V and Talla E | | | | Molecular phylogenetics of Sarcolaenaceae (Malvales), Madagascar's largest endemic plant family | Aubriot X, Soulebeau A, Haevermans T, Schatz GE, Cruaud C and Lowry PP | | |
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