| Complete genome sequence of Shewanella benthica DB21MT-2, an obligate piezophilic bacterium isolated from the deepest Mariana Trench sediment | Zhang WJ, Cui XH, Chen LH, Yang J, Li XG, Zhang C, Barbe V, Mangenot S, Fouteau S, Guerin T, Kato C and Wu LF | |  | | 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 | | | | Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters | Arsene-Ploetze F, Chiboub O, Lievremont D, Farasin J, Freel KC, Fouteau S and Barbe 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 | | | | Extended-spectrum beta-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins | Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S, Barbe V, Roche D, Cruveiller S, Medigue C, Castellanos M, Decre D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G and Denamur E | | | | 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 | | | | Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean | Chen NWG, Serres-Giardi L, Ruh M, Briand M, Bonneau S, Darrasse A, Barbe V, Gagnevin L, Koebnik R and Jacques MA | | | | Common Bean Subtelomeres Are Hot Spots of Recombination and Favor Resistance Gene Evolution | Chen NWG, Thareau V, Ribeiro T, Magdelenat G, Ashfield T, Innes RW, Pedrosa-Harand A and Geffroy V | | | | Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs | Dias GM, Bidault A, Le Chevalier P, Choquet G, Sarkissian CD, Orlando L, Medigue C, Barbe V, Mangenot S, Thompson CC, Thompson FL, Jacq A, Pichereau V and Paillard 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 | | | | Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9(T) to Adapt to Macroalgal Niches | Gobet A, Barbeyron T, Matard-Mann M, Magdelenat G, Vallenet D, Duchaud E and Michel G | | | | 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 | | | | 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 | | | | Modeling trophic dependencies and exchanges among insects' bacterial symbionts in a host-simulated environment | Opatovsky I, Santos-Garcia D, Ruan ZP, Lahav T, Ofaim S, Mouton L, Barbe V, Jiang JD, Zchori-Fein E and Freilich S | | | | 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 | | | | Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy | Sugier K, Vacherie B, Cornils A, Wincker P, Jamet JL and Madoui MA | | | | Status of coral reefs of Upolu (Independent State of Samoa) in the South West Pacific and recommendations to promote resilience and recovery of coastal ecosystems | Ziegler M, Quere G, Ghiglione JF, Iwankow G, Barbe V, Boissin E, Wincker P, Planes S and Voolstra CR | | | | A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications | Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, Jaillon O, Not F, Nunes F, Payri C, Wincker P and Barbe V | | | | Biogeography and diversity of Collodaria (Radiolaria) in the global ocean | Biard T, Bigeard E, Audic S, Poulain J, Gutierrez-Rodriguez A, Pesant S, Stemmann L and Not F | | | | Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21 | Bringel F, Postema CP, Mangenot S, Bibi-Triki S, Chaignaud P, Farhan Ul Haque M, Gruffaz C, Hermon L, Louhichi Y, Maucourt B, Muller EEL, Nadalig T, Lajus A, Rouy Z, Medigue C, Barbe V, Janssen DB and Vuilleumier S | | | | 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 | | | | Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium | Chaignaud P, Maucourt B, Weiman M, Alberti A, Kolb S, Cruveiller S, Vuilleumier S and Bringel F | | | | Flipping chromosomes in deep-sea archaea | Cossu M, Badel C, Catchpole R, Gadelle D, Marguet E, Barbe V, Forterre P and Oberto J | | | | Towards standards for human fecal sample processing in metagenomic studies | Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, Vlieg JVH, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao LP, Zoetendal EG, Ehrlich SD, Dore J and Bork P | | | | The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria | Ji BY, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, Mangenot S, Gagnot S, Philippe N, Pradel N, Zhang LC, Tempel S, Li Y, Medigue C, Henrissat B, Coutinho PM, Barbe V, Talla E and Wu LF | | | | Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium | Lassalle F, Penel R, Penel S, Chapulliot D, Barbe V, Dubost A, Calteau A, Vallenet D, Mornico D, Bigot T, Gueguen L, Vial L, Muller D, Daubin V and Nesme X | | | | New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona | Madoui MA, Poulain J, Sugier K, Wessner M, Noel B, Berline L, Labadie K, Cornils A, Blanco-Bercial L, Stemmann L, Jamet JL and Wincker P | | | | Insights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains | Pancrace C, Barny MA, Ueoka R, Calteau A, Scalvenzi T, Pedron J, Barbe V, Piel J, Humbert JF and Gugger M | | | | The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms | Perez-Pascual D, Lunazzi A, Magdelenat G, Rouy Z, Roulet A, Lopez-Roques C, Larocque R, Barbeyron T, Gobet A, Michel G, Bernardet JF and Duchaud E | | | | 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 | | | | 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 | | | | The complete mitochondrial genome of Acanthastrea maxima (Cnidaria, Scleractinia, Lobophylliidae) | Arrigoni R, Vacherie B, Benzoni F and Barbe V | | | | A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications | Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, Jaillon O, Not F, Nunes F, Payri C, Wincker P and Barbe V | | | | 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 | | | | The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis | Belda E, van Heck RGA, Lopez-Sanchez MJ, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, dos Santos V, de Lorenzo V, Danchin A and Medigue C | | | | Polysaccharide utilisation loci of Bacteroidetes from two contrasting open ocean sites in the North Atlantic | Bennke CM, Kruger K, Kappelmann L, Huang SX, Gobet A, Schuler M, Barbe VE, Fuchs BM, Michel G, Teeling H and Amann RI | | | | 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 | | | | 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 | | | | Microbial Degradation of a Recalcitrant Pesticide: Chlordecone | Chaussonnerie S, Saaidi PL, Ugarte E, Barbance A, Fossey A, Barbe V, Gyapay G, Bruls T, Chevalier M, Couturat L, Fouteau S, Muselet D, Pateau E, Cohen GN, Fonknechten N, Weissenbach J and Le Paslier D | | | | Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton | Cornejo-Castillo FM, Cabello AM, Salazar G, Sanchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R and Acinas SG | | | | 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 | | | | 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 | | | Complete Genome Sequence of Mycoplasma mycoides subsp. mycoides T1/44, a Vaccine Strain against Contagious Bovine Pleuropneumonia | Gourgues G, Barre A, Beaudoing E, Weber J, Magdelenat G, Barbe V, Schieck E, Jores J, Vashee S, Blanchard A, Lartigue C and Sirand-Pugnet P | | | | Plankton networks driving carbon export in the oligotrophic ocean | Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum JR, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G and Tara Oceans Consortium C | | | | 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 | | | | Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes | Lebrigand K, He LD, Thakur N, Arguel MJ, Polanowska J, Henrissat B, Record E, Magdelenat G, Barbe V, Raffaele S, Barbry P and Ewbank JJ | | | | Insights into global diatom distribution and diversity in the world's ocean | Malviya S, Scalco E, Audic S, Vincenta F, Veluchamy A, Poulain J, Wincker P, Iudicone D, de Vargas C, Bittner L, Zingone A and Bowler C | | | | "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 | | | | The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LHP1 Function in Concert to Regulate the Transcription of Stress-Responsive Genes | Molitor AM, Latrasse D, Zytnicki M, Andrey P, Houba-Herin N, Hachet M, Battail C, Del Prete S, Alberti A, Quesneville E and Gaudin V | | | | Parasitic wasps have domesticated viruses repeatedly during their evolution | Pichon A, Bezier A, Barbe V, Drezen JM and Volkoff AN | | | | 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 | | | | Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200 | Zhang SD, Santini CL, Zhang WJ, Barbe V, Mangenot S, Guyomar C, Garel M, Chen HT, Li XG, Yin QJ, Zhao Y, Armengaud J, Gaillard JC, Martini S, Pradel N, Vidaud C, Alberto F, Medigue C, Tamburini C and Wu LF | | | | Non-invasive prenatal testing for trisomy 21 based on analysis of cell-free fetal DNA circulating in the maternal plasma | Alberti A, Salomon LJ, Le Lorc'h M, Couloux A, Bussieres L, Goupil S, Malan V, Pelletier E, Hyon C, Vialard F, Rozenberg P, Bouhanna P, Oury JF, Schmitz T, Romana S, Weissenbach J, Vekemans M and Ville Y | | | | 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 | | | | Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data | Benjelloun B, Alberto FJ, Streeter I, Boyer F, Coissac E, Stucki S, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, Flicek P, Joost S, Taberlet P, Pompanon F and NextGen C | | | | The Genome of the Nucleopolyhedrosis-Causing Virus from Tipula oleracea Sheds New Light on the Nudiviridae Family | Bezier A, Theze J, Gavory F, Gaillard J, Poulain J, Drezen JM and Herniou EA | | | | 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 | | | | Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations | Chateigner A, Bezier A, Labrousse C, Jiolle D, Barbe V and Herniou EA | | | | Transcriptomic response of Manduca sexta immune tissues to parasitization by the bracovirus associated wasp Cotesia congregata | Chevignon G, Cambier S, Da Silva C, Poulain J, Drezen JM, Huguet E and Moreau SJM | | | | Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides | Czernic P, Gully D, Cartieaux F, Moulin L, Guefrachi I, Patrel D, Pierre O, Fardoux J, Chaintreuil C, Nguyen P, Gressent F, Da Silva C, Poulain J, Wincker P, Rofidal V, Hem S, Barriere Q, Arrighi JF, Mergaert P and Giraud E | | | | Eukaryotic plankton diversity in the sunlit ocean | de Vargas C, Audic S, Henry N, Decelle J, Mahe F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horak A, Jaillon O, Lima-Mendez G, Lukes J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E and Tara Oceans C | | | | Thiomonas sp CB2 is able to degrade urea and promote toxic metal precipitation in acid mine drainage waters supplemented with urea | Farasin J, Andres J, Casiot C, Barbe V, Faerber J, Halter D, Heintz D, Koechler S, Lievremont D, Ugan R, Marchal M, Plewniak F, Seby F, Bertin PN and Arsene-Ploetze F | | | | Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi | Fontanillas E, Hood ME, Badouin H, Petit E, Barbe V, Gouzy J, de Vienne DM, Aguileta G, Poulain J, Wincker P, Chen ZH, Toh SS, Cuomo CA, Perlin MH, Gladieux P and Giraud T | | | | Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas | Freel KC, Krueger MC, Farasin J, Brochier-Armanet C, Barbe V, Andres J, Cholley PE, Dillies MA, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppee JY, Bertin PN, Heipieper HJ and Arsene-Ploetze F | | | | AAC(3)-XI, a New Aminoglycoside 3-N-Acetyltransferase from Corynebacterium striatum | Galimand M, Fishovitz J, Lambert T, Barbe V, Zajicek J, Mobashery S and Courvalin P | | | | Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges | Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L and Pruvost O | | | | A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters | Goudenege D, Travers MA, Lemire A, Petton B, Haffner P, Labreuche Y, Tourbiez D, Mangenot S, Calteau A, Mazel D, Nicolas JL, Jacq A and Le roux F | Environmental Microbiology 17 (11), 4189-4199, 2015 | | | Arsenic hypertolerance in the protist Euglena mutabilis is mediated by specific transporters and functional integrity maintenance mechanisms | Halter D, Andres J, Plewniak F, Poulain J, Da Silva C, Arsene-Ploetze F and Bertin PN | | | | Deciphering metatranscriptomic data | Kopylova E, Noe L, Da Silva C, Berthelot J-F, Alberti A, Aury J-M and Touzet H | | | | Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii | Loux V, Mariadassou M, Almeida S, Chiapello H, Hammani A, Buratti J, Gendrault A, Barbe V, Aury JM, Deutsch SM, Parayre S, Madec MN, Chuat V, Jan G, Peterlongo P, Azevedo V, Le Loir Y and Falentin H | | | | 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 | | | | Recurrent DNA virus domestication leading to different parasite virulence strategies | Pichon A, Bezier A, Urbach S, Aury J-M, Jouan V, Ravallec M, Guy J, Cousserans F, Theze J, Gauthier J, Demettre E, Schmieder S, Wurmser F, Sibut V, Poirie M, Colinet D, da Silva C, Couloux A, Barbe V, Drezen J-M and Volkoff A-N | | | | Draft Genome Sequence of Xanthomonas sacchari Strain LMG 476 | Pieretti I, Bolot S, Carrere S, Barbe V, Cociancich S, Rott P and Royer M | | | | Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome | Pingault L, Choulet F, Alberti A, Glover N, Wincker P, Feuillet C and Paux E | | | | Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts | Rollat-Farnier PA, Santos-Garcia D, Rao Q, Sagot MF, Silva FJ, Henri H, Zchori-Fein E, Latorre A, Moya A, Barbe V, Liu SS, Wang XW, Vavre F and Mouton L | | | | Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels | Sayavedra L, Kleiner M, Ponnudurai R, Wetzel S, Pelletier E, Barbe V, Satoh N, Shoguchi E, Fink D, Breusing C, Reusch TBH, Rosenstiel P, Schilhabel MB, Becher D, Schweder T, Markert S, Dubilier N and Petersen JM | | | | 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 | | | | 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 | | | | Characterization of a P1-Like Bacteriophage Carrying an SHV-2 Extended-Spectrum beta-Lactamase from an Escherichia coli Strain | Billard-Pomares T, Fouteau S, Jacquet ME, Roche D, Barbe V, Castellanos M, Bouet JY, Cruveiller S, Medigue C, Blanco J, Clermont O, Denamur E and Branger C | | | | 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 | | | | 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 | | | | Population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons | Gilbert C, Chateigner A, Ernenwein L, Barbe V, Bezier A, Herniou EA and Cordaux R | | | | Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens | Grandaubert J, Lowe RGT, Soyer JL, Schoch CL, de Wouw APV, Fudal I, Robbertse B, Lapalu N, Links MG, Ollivier B, Linglin J, Barbe V, Mangenot S, Cruaud C, Borhan H, Howlett BJ, Balesdent MH and Rouxel T | | | | Draft Genome Sequence of Propane- and Butane-Oxidizing Actinobacterium Rhodococcus ruber IEGM 231 | Ivshina IB, Kuyukina MS, Krivoruchko AV, Barbe V and Fischer C | | | | Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp QH-2 strain | Ji BY, Zhang SD, Arnoux P, Rouy Z, Alberto F, Philippe N, Murat D, Zhang WJ, Rioux JB, Ginet N, Sabaty M, Mangenot S, Pradel N, Tian JS, Yang J, Zhang LC, Zhang WY, Pan HM, Henrissat B, Coutinho PM, Li Y, Xiao T, Medigue C, Barbe V, Pignol D, Talla E and Wu LF | | | | The complete genome of Blastobotrys (Arxula) adeninivorans LS3-a yeast of biotechnological interest | Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Boer E, Gabaldon T, Cruz JA, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski PP, Haehnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard GF, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman DJ, Stein N, Straub ML, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet JL, Wincker P, Scholz U and Neuveglise C | | | | Establishment and analysis of a reference transcriptome for Spodoptera frugiperda | Legeai F, Gimenez S, Duvic B, Escoubas JM, Grenet ASG, Blanc F, Cousserans F, Seninet I, Bretaudeau A, Mutuel D, Girard PA, Monsempes C, Magdelenat G, Hilliou F, Feyereisen R, Ogliastro M, Volkoff AN, Jacquin-Joly E, d'Alencon E, Negre N and Fournier P | | | | Comparative analysis of Klebsiella pneumoniae genomes identifies a phospholipase D family protein as a novel virulence factor | Lery LMS, Frangeul L, Tomas A, Passet V, Almeida AS, Bialek-Davenet S, Barbe V, Bengoechea JA, Sansonetti P, Brisse S and Tournebize R | | | | Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities | Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P and Acinas SG | | | | Ancient hybridizations among the ancestral genomes of bread wheat | Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, Jakobsen KS, Wulff BBH, Steuernagel B, Mayer KFX, Olsen OA, Rogers J, Dolezel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P, Endo TR, Kubalakova M, Cihalikova J, Dubska Z, Vrana J, Sperkova R, Simkova H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh NK, Khurana J, Akhunov E, Choulet F, Alberti A, Barbe V, Wincker P, Kanamori H, Kobayashi F, Itoh T, Matsumoto T, Sakai H, Tanaka T, Wu JZ, Ogihara Y, Handa H, Maclachlan PR, Sharpe A, Klassen D, Edwards D, Batley J, Lien S, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Martis MM, Mascher M, Chapman J, Poland JA, Scholz U, Barry K, Waugh R, Rokhsar DS, Muehlbauer GJ, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca AM, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader KC, Rimbert H, Wang SC, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B, Praud S and Int Wheat Genome S | | |
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