| 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 | | | | 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 | | | | 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 | | | | Global repositioning of transcription start sites in a plant-fermenting bacterium | Boutard M, Ettwiller L, Cerisy T, Alberti A, Labadie K, Salanoubat M, Schildkraut I and Tolonen AC | | | | Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium | Gerbore J, Brutel A, Lemainque A, Mairey B, Medigue C, Vallenet D, Lefort F and Grizard D | Genome announcements 4 (2), , 2016 | | | 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 | | | | Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding | Le Bescot N, Mahe F, Audic S, Dimier C, Garet MJ, Poulain J, Wincker P, de Vargas C and Siano R | | | | 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 | | | | 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 | | | | Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae) | Roquet C, Coissac E, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J and Lavergne S | | | | 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 | | | | Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species | Alves-Carvalho S, Aubert G, Carrere S, Cruaud C, Brochot AL, Jacquin F, Klein A, Martin C, Boucherot K, Kreplak J, da Silva C, Moreau S, Gamas P, Wincker P, Gouzy J and Burstin J | | | | Transcriptome analyses to investigate symbiotic relationships between marine protists | Balzano S, Corre E, Decelle J, Sierra R, Wincker P, Da Silva C, Poulain J, Pawlowski J and Not F | | | | 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 | | | | Community assembly on remote islands: a comparison of Hawaiian and Mascarene spiders | Casquet J, Bourgeois YXC, Cruaud C, Gavory F, Gillespie RG and Thebaud C | | | | Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes | Clerissi C, Desdevises Y, Romac S, Audic S, de Vargas C, Acinas SG, Casotti R, Poulain J, Wincker P, Hingamp P, Ogata H and Grimsley N | | | | Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species? | Dumas P, Legeai F, Lemaitre C, Scaon E, Orsucci M, Labadie K, Gimenez S, Clamens AL, Henri H, Vavre F, Aury JM, Fournier P, Kergoat GJ and d'Alencon E | | | | 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 | | | Improving biodiversity assessment of anuran amphibians using DNA barcoding of tadpoles. Case studies from Southeast Asia | Grosjean S, Ohler A, Chuaynkern Y, Cruaud C and Hassanin A | | | | In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba | Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Coute Y, Abergel C and Claverie JM | | | | Genome assembly using Nanopore-guided long and error-free DNA reads | Madoui MA, Engelen S, Cruaud C, Belser C, Bertrand L, Alberti A, Lemainque A, Wincker P and Aury JM | | | | Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts | Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, Souciet JL, Gabaldon T, Tinsley CR and Casaregola S | | | | Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts (vol 5, 11571, 2015) | Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, Souciet JL, Gabaldon T, Tinsley CR and Casaregola S | Scientific Reports 5 (), , 2015 | | | An inter-ocean comparison of coral endemism on seamounts: the case of Chrysogorgia | Pante E, France SC, Gey D, Cruaud C and Samadi S | | | | Structure and function of the global ocean microbiome | Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P and Tara Oceans C | | | | Improving soil bacterial taxa-area relationships assessment using DNA meta-barcoding | Terrat S, Dequiedt S, Horrigue W, Lelievre M, Cruaud C, Saby NPA, Jolivet C, Arrouays D, Maron PA, Ranjard L and Prevost-Boure NC | | | | Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton | von Dassow P, John U, Ogata H, Probert I, Bendif E, Kegel JU, Audic S, Wincker P, Da Silva C, Claverie JM, Doney S, Glover DM, Flores DM, Herrera Y, Lescot M, Garet-Delmas MJ and de Vargas C | | | | Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data | Alberti A, Belser C, Engelen S, Bertrand L, Orvain C, Brinas L, Cruaud C, Giraut L, Da Silva C, Firmo C, Aury JM and Wincker P | | | | The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates | Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noel B, Bento P, Da Silva C, Labadie K, Alberti A, Aury JM, Louis A, Dehais P, Bardou P, Montfort J, Klopp C, Cabau C, Gaspin C, Thorgaard GH, Boussaha M, Quillet E, Guyomard R, Galiana D, Bobe J, Volff JN, Genet C, Wincker P, Jaillon O, Crollius HR and Guiguen Y | | | | Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome | Chalhoub B, Denoeud F, Liu SY, Parkin IAP, Tang HB, Wang XY, Chiquet J, Belcram H, Tong CB, Samans B, Correa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao MX, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan GY, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHD, Chalabi S, Hu Q, Fan CC, Tollenaere R, Lu YH, Battail C, Shen JX, Sidebottom CHD, Wang XF, Canaguier A, Chauveau A, Berard A, Deniot G, Guan M, Liu ZS, Sun FM, Lim YP, Lyons E, Town CD, Bancroft I, Wang XW, Meng JL, Ma JX, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou YM, Hua W, Sharpe AG, Paterson AH, Guan CY and Wincker P | | | | Characterization of Novel Polycyclic Aromatic Hydrocarbon Dioxygenases from the Bacterial Metagenomic DNA of a Contaminated Soil | Chemerys A, Pelletier E, Cruaud C, Martin F, Violet F and Jouanneau Y | | | | Functional Annotation of Cotesia congregata Bracovirus: Identification of Viral Genes Expressed in Parasitized Host Immune Tissues | Chevignon G, Theze J, Cambier S, Poulain J, Da Silva C, Bezier A, Musset K, Moreau SJM, Drezen J-M and Huguet E | | | | Structural and functional partitioning of bread wheat chromosome 3B | Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury J-M, Mayer K, Berges H, Quesneville H, Wincker P and Feuillet C | | | | Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine Samples by Using High-Throughput Sequencing Analyses of PCR-Amplified DNA Polymerase and Major Capsid Protein Genes | Clerissi C, Grimsley N, Ogata H, Hingamp P, Poulain J and Desdevises Y | | | | Identification of the main venom protein components of Aphidius ervi, a parasitoid wasp of the aphid model Acyrthosiphon pisum | Colinet D, Anselme C, Deleury E, Mancini D, Poulain J, Azema-Dossat C, Belghazi M, Tares S, Pennacchio F, Poirie M and Gatti JL | | | | Mapping the Epigenetic Basis of Complex Traits | Cortijo S, Wardenaar R, Colome-Tatche M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V and Johannes F | | | | Organization and evolution of transposable elements along the bread wheat chromosome 3B | Daron J, Glover N, Pingault L, Theil S, Jamilloux V, Paux E, Barbe V, Mangenot S, Alberti A, Wincker P, Quesneville H, Feuillet C and Choulet F | | | | The coffee genome provides insight into the convergent evolution of caffeine biosynthesis | Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng CF, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joet T, Labadie K, Lan TY, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Munoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P and Lashermes P | | | | Phylogeny and taxonomy of Syngonanthus and Comanthera (Eriocaulaceae): Evidence from expanded sampling | Echternacht L, Sano PT, Bonilla C, Cruaud C, Couloux A and Dubuisson JY | | | | Insights on the Evolution of Plant Succulence from a Remarkable Radiation in Madagascar (Euphorbia) | Evans M, Aubriot X, Hearn D, Lanciaux M, Lavergne S, Cruaud C, Lowry PP and Haevermans T | | | | The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome | Formey D, Sallet E, Lelandais-Briere C, Ben C, Bustos-Sanmamed P, Niebel A, Frugier F, Combier JP, Debelle F, Hartmann C, Poulain J, Gavory F, Wincker P, Roux C, Gentzbittel L, Gouzy J and Crespi M | | | | TE-Tracker: systematic identification of transposition events through whole-genome resequencing | Gilly A, Etcheverry M, Madoui MA, Guy J, Quadrana L, Alberti A, Martin A, Heitkam T, Engelen S, Labadie K, Le Pen J, Wincker P, Colot V and Aury JM | | |
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