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Laboratoire

Laboratoire de séquençage

Publications



Publié le 25 juin 2018
  
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
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
Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle
Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsan K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, Zifcakova L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury JM, Wincker P, Grigoriev IV, Bonfante P and Martin FM
Genome evolution across 1,011 Saccharomyces cerevisiae isolates
Peter J, De Chiara M, Friedrich A, Yue JX, Pflieger D, Bergstrom A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G and Schacherer J
Oak genome reveals facets of long lifespan
Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholome J, Faivre-Rampant P, Kohler A, Leple JC, Chantret N, Chen J, Dievart A, Alaeitabar T, Barbe V, Belser C, Berges H, Bodenes C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rue O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A and Salse J
The Rosa genome provides new insights into the domestication of modern roses
Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C, Carrere S, Caissard JC, Couloux A, Cottret L, Aury JM, Szecsi J, Latrasse D, Madoui MA, Francois L, Fu XP, Yang SH, Dubois A, Piola F, Larrieu A, Perez M, Labadie K, Perrier L, Govetto B, Labrousse Y, Villand P, Bardoux C, Boltz V, Lopez-Roques C, Heitzler P, Vernoux T, Vandenbussche M, Quesneville H, Boualem A, Bendahmane A, Liu C, Le Bris M, Salse J, Baudino S, Benhamed M, Wincker P and Bendahmane M
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
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
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
Venom gland extract is not required for successful parasitism in the polydnavirus-associated endoparasitoid Hyposoter didymator (Hym. Ichneumonidae) despite the presence of numerous novel and conserved venom proteins (vol 43, pg 292, 2013)
Doremus T, Urbach S, Jouan V, Cousserans F, Ravallec M, Demettre E, Wajnberg E, Poulain J, Azema-Dossat C, Darboux I, Escoubas JM, Colinet D, Gatti JL, Poirie M and Volkoff AN
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
Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates
Godard BG, Coolen M, Le Panse S, Gombault A, Ferreiro-Galve S, Laguerre L, Lagadec R, Wincker P, Poulain J, Da Silva C, Kuraku S, Carre W, Boutet A and Mazan S
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
Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis in Podospora anserina
Grognet P, Bidard F, Kuchly C, Tong LCH, Coppin E, Benkhali JA, Couloux A, Wincker P, Debuchy R and Silar P
Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus
Humily F, Farrant GK, Marie D, Partensky F, Mazard S, Perennou M, Labadie K, Aury JM, Wincker P, Segui AN, Scanlan DJ and Garczarek L
Forest refugia and riverine barriers promote diversification in the West African pygmy shrew (Crocidura obscurior complex, Soricomorpha)
Jacquet F, Nicolas V, Colyn M, Kadjo B, Hutterer R, Decher J, Akpatou B, Cruaud C and Denys C
Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology
Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Coute Y, Rivkina E, Abergel C and Claverie JM
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
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
Mayer KFX, 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, Olsen OA, Sandve SR, Lien S, Steuernagel B, Wulff B, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Pfeifer M, Spannagl M, 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 Iwgsc
Evolution within the nuthatches (Sittidae: Aves, Passeriformes): molecular phylogeny, biogeography, and ecological perspectives
Pasquet E, Barker FK, Martens J, Tillier A, Cruaud C and Cibois A
The Spatiotemporal Program of DNA Replication Is Associated with Specific Combinations of Chromatin Marks in Human Cells
Picard F, Cadoret JC, Audit B, Arneodo A, Alberti A, Battail C, Duret L and Prioleau MN
Complete genome sequence of invertebrate iridovirus IIV-25 isolated from a blackfly larva
Piegu B, Guizard S, Spears T, Cruaud C, Couloux A, Bideshi DK, Federici BA and Bigot Y
Complete genome sequence of invertebrate iridovirus IIV30 isolated from the corn earworm, Helicoverpa zea
Piegu B, Guizard S, Spears T, Cruaud C, Couloux A, Bideshi DK, Federici BA and Bigot Y
Journal of Invertebrate Pathology 116 (), 43-47, 2014
Complete genome sequence of invertebrate iridovirus IIV22A, a variant of IIV22, isolated originally from a blackfly larva
Piegu B, Guizard S, Tan YP, Cruaud C, Couloux A, Bideshi DK, Federici BA and Bigot Y
Genome sequence of a crustacean iridovirus, IIV31, isolated from the pill bug, Armadillidium vulgare
Piegu B, Guizard S, Yeping T, Cruaud C, Asgari S, Bideshi DK, Federici BA and Bigot Y
The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants
Porcel BM, Denoeud F, Opperdoes F, Noel B, Madoui MA, Hammarton TC, Field MC, Da Silva C, Couloux A, Poulain J, Katinka M, Jabbari K, Aury JM, Campbell DA, Cintron R, Dickens NJ, Docampo R, Sturm NR, Koumandou VL, Fabre S, Flegontov P, Lukes J, Michaeli S, Mottram JC, Szoor B, Zilberstein D, Bringaud F, Wincker P and Dollet M
A Phylogenetic Re-Analysis of Groupers with Applications for Ciguatera Fish Poisoning
Schoelinck C, Hinsinger DD, Dettai A, Cruaud C and Justine JL
Genome-defence small RNAs exapted for epigenetic mating-type inheritance
Singh DP, Saudemont B, Guglielmi G, Arnaiz O, Gout JF, Prajer M, Potekhin A, Przybos E, Aubusson-Fleury A, Bhullar S, Bouhouche K, Lhuillier-Akakpo M, Tanty V, Blugeon C, Alberti A, Labadie K, Aury JM, Sperling L, Duharcourt S and Meyer E
Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach
Stuani L, Lechaplais C, Salminen AV, Segurens B, Durot M, Castelli V, Pinet A, Labadie K, Cruveiller S, Weissenbach J, de Berardinis V, Salanoubat M and Perret A
Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection
Talhinhas P, Azinheira HG, Vieira B, Loureiro A, Tavares S, Batista D, Morin E, Petitot AS, Paulo OS, Poulain J, Da Silva C, Duplessis S, Silva MD and Fernandez D
Recognition of a new species of Kallymenia (Gigartinales, Rhodophyta) from Croatia (Mediterranean Sea) based on morphology and DNA barcode
Verges A, Gey D, Utge J, Cruaud C and Le Gall L
Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis
Watanabe J, Hattori M, Berriman M, Lehane MJ, Hall N, Solano P, Aksoy S, Hide W, Toure Y, Attardo GM, Darby AC, Toyoda A, Hertz-Fowler C, Larkin DM, Cotton JA, Sanders MJ, Swain MT, Quail MA, Inoue N, Ravel S, Taylor TD, Srivastava TP, Sharma V, Warren W, Wilson RK, Suzuki Y, Lawson D, Hughes DST, Megy K, Masiga DK, Mireji PO, Hansen IA, Van den Abbeele J, Benoit JB, Bourtzis K, Obiero GFO, Robertson HM, Jones JW, Zhou JJ, Field LM, Friedrich M, Nyanjom SRG, Telleria EL, Caljon G, Ribeiro JMC, Acosta-Serrano A, Ooi CP, Rose C, Price DP, Haines LR, Christoffels A, Sim C, Pham DQD, Denlinger DL, Geiser DL, Omedo IA, Winzerling JJ, Peyton JT, Marucha KK, Jonas M, Meuti ME, Rawlings ND, Zhang QR, Macharia RW, Michalkova V, Dashti ZJS, Baumann AA, Gade G, Marco HG, Caers J, Schoofs L, Riehle MA, Hu WQ, Tu ZJ, Tarone AM, Malacrida AR, Kibet CK, Scolari F, Koekemoer JJO, Willis J, Gomulski LM, Falchetto M, Scott MJ, Fu SH, Sze SH, Luiz T, Weiss B, Walshe DP, Wang JW, Wamalwa M, Mwangi S, Ramphul UN, Snyder AK, Brelsfoard CL, Thomas GH, Tsiamis G, Arensburger P, Rio RVM, Macdonald SJ, Panji S, Kruger A, Benkahla A, Balyeidhusa ASP, Msangi A, Okoro CK, Stephens D, Stanley EJ, Mpondo F, Wamwiri F, Mramba F, Siwo G, Githinji G, Harkins G, Murilla G, Lehvaslaiho H, Malele I, Auma JE, Kinyua JK, Ouma J, Okedi L, Manga L, Aslett M, Koffi M, Gaunt MW, Makgamathe M, Mulder N, Manangwa O, Abila PP, Wincker P, Gregory R, Bateta R, Sakate R, Ommeh S, Lehane S, Imanishi T, Osamor VC, Kawahara Y and Iggi
Fifty thousand years of Arctic vegetation and megafaunal diet
Willerslev E, Davison J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergard M, Gussarova G, Haile J, Craine J, Gielly L, Boessenkool S, Epp LS, Pearman PB, Cheddadi R, Murray D, Brathen KA, Yoccoz N, Binney H, Cruaud C, Wincker P, Goslar T, Alsos IG, Bellemain E, Brysting AK, Elven R, Sonstebo JH, Murton J, Sher A, Rasmussen M, Ronn R, Mourier T, Cooper A, Austin J, Moller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RDE, Gilbert MTP, Kjaer KH, Orlando L, Brochmann C and Taberlet P
DNA barcoding in a biodiversity hot spot: potential value for the identification of Malagasy Euphorbia L. listed in CITES Appendices I and II
Aubriot X, Lowry PP, Cruaud C, Couloux A and Haevermans T
Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata: insights into the evolutionary dynamics of bracoviruses
Bezier A, Louis F, Jancek S, Periquet G, Theze J, Gyapay G, Musset K, Lesobre J, Lenoble P, Dupuy C, Gundersen-Rindal D, Herniou EA and Drezen JM
Molecular evidence for novel Cantharellus (Cantharellales, Basidiomycota) from tropical African miombo woodland and a key to all tropical African chanterelles
Buyck B, Kauff F, Cruaud C and Hofstetter V
Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest
Coince A, Cael O, Bach C, Lengelle J, Cruaud C, Gavory F, Morin E, Murat C, Marcais B and Buee M
Extensive inter- and intraspecific venom variation in closely related parasites targeting the same host: the case of Leptopilina parasitoids of Drosophila
Colinet D, Deleury E, Anselme C, Cazes D, Poulain J, Azema-Dossat C, Belghazi M, Gatti JL and Poirie M
Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida
Collen J, Porcel B, Carre W, Ball SG, Chaparro C, Tonon T, Barbeyron T, Michel G, Noel B, Valentin K, Elias M, Artiguenave F, Arun A, Aury JM, Barbosa-Neto JF, Bothwell JH, Bouget FY, Brillet L, Cabello-Hurtado F, Capella-Gutierrez S, Charrier B, Cladiere L, Cock JM, Coelho SM, Colleoni C, Czjzek M, Da Silva C, Delage L, Denoeud F, Deschamps P, Dittami SM, Gabaldon T, Gachon CMM, Groisillier A, Herve C, Jabbari K, Katinka M, Kloareg B, Kowalczyk N, Labadie K, Leblanc C, Lopez PJ, McLachlan DH, Meslet-Cladiere L, Moustafa A, Nehr Z, Collen PN, Panaud O, Partensky F, Poulain J, Rensing SA, Rousvoal S, Samson G, Symeonidi A, Weissenbach J, Zambounis A, Wincker P and Boyen C
Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining
Danchin EGJ, Arguel MJ, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso MN, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F and Abad P
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