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Jean-Marc AURY

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Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

Ana Paula Zotta Mota , Georgios Koutsovoulos , Laetitia Perfus-Barbeoch , Evelin Despot-Slade , Karine Labadie
Nature Communications, 2024, 15 (1), pp.773. ⟨10.1038/s41467-024-44914-y⟩
Journal articles hal-04489824v1
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Imputed genomes of historical horses provide insights into modern breeding

Evelyn T Todd , Aurore Fromentier , Richard Sutcliffe , Yvette Running , Horse Collin
iScience, 2023, 26 (7), pp.107104. ⟨10.1016/j.isci⟩
Journal articles hal-04242127v1
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Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology

Gregoire Le Provost , Céline Lalanne , Isabelle Lesur , Jean-Marc Louvet , Sylvain Delzon
BMC Plant Biology, 2023, 23 (108), ⟨10.1186/s12870-023-04069-2⟩
Journal articles hal-04003618v1
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Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes

Ferdinand Marlétaz , Arnaud Couloux , Julie Poulain , Karine Labadie , Corinne da Silva
Cell Genomics, 2023, 3 (4), pp.100295. ⟨10.1016/j.xgen.2023.100295⟩
Journal articles hal-04093287v1
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DNA methylation-based profiling of horse archaeological remains for age-at-death and castration

Xuexue Liu , Andaine Seguin- Orlando , Lorelei Chauvey , Gaëtan Tressières , Laure Tonasso-Calvie
iScience, 2023, 26 (3), pp.106144. ⟨10.1016/j.isci.2023.106144⟩
Journal articles cea-04286440v1
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Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Caroline Belser , Julie Poulain , Karine Labadie , Frederick Gavory , Adriana Alberti
Scientific Data , 2023, 10 (1), pp.326. ⟨10.1038/s41597-023-02204-0⟩
Journal articles hal-04176297v1

Estimation of contemporary effective population size in plant populations: limitations of genomic datasets

Roberta Gargiulo , Véronique Decroocq , Santiago González-Martínez , Ivan Paz-Vinas , Jean-Marc Aury
Tree Genetics and Genomes, 2023, 15 (5), pp.76. ⟨10.1101/2023.07.18.549323⟩
Journal articles hal-04230362v1

Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood

Stefanie Wagner , Andaine Seguin-Orlando , Jean-Charles Leplé , Thibault Leroy , Céline Lalanne
Molecular Ecology, 2023, ⟨10.1111/mec.16859⟩
Journal articles hal-04158430v1
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Shared pedigree relationships and transmission of unreduced gametes in cultivated banana

Guillaume Martin , Franc-Christophe Baurens , Karine Labadie , Catherine Hervouet , Frédéric Salmon
Annals of Botany, 2023, 131 (7), pp.1149-1161. ⟨10.1093/aob/mcad065⟩
Journal articles hal-04361041v1
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Pervasive tandem duplications and convergent evolution shape coral genomes

Benjamin Noel , France Denoeud , Alice Rouan , Carol Buitrago-López , Laura Capasso
Genome Biology, 2023, 24 (1), pp.123. ⟨10.1186/s13059-023-02960-7⟩
Journal articles hal-04117388v1
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Host transcriptomic plasticity and photosymbiotic fidelity underpin $Pocillopora$ acclimatization across thermal regimes in the Pacific Ocean

Eric J Armstrong , Julie Lê-Hoang , Quentin Carradec , Jean-Marc Aury , Benjamin Noel
Nature Communications, 2023, 14, pp.3056. ⟨10.1038/s41467-023-38610-6⟩
Journal articles cea-04171796v1
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Early dispersal of domestic horses into the Great Plains and northern Rockies

William Timothy Treal Taylor , Pablo Librado , Mila Hunska Tašunke Icu , Carlton Shield Chief Gover , Jimmy Arterberry
Science, 2023, 379 (6639), pp.1316-1323. ⟨10.1126/science.adc9691⟩
Journal articles hal-04065852v1
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Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Alice Rouan , Melanie Pousse , Nadir Djerbi , Barbara Porro , Guillaume Bourdin
Nature Communications, 2023, 14 (1), pp.3038. ⟨10.1038/s41467-023-38499-1⟩
Journal articles cea-04171809v1

Origin and evolution of the triploid cultivated banana genome

Xiuxiu Li , Sheng Yu , Zhihao Cheng , Xiaojun Chang , Yingzi Yun
Nature Genetics, 2023, ⟨10.1038/s41588-023-01589-3⟩
Journal articles hal-04387017v1
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Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea

Guillaume Martin , Aurélien Cottin , Franc‐christophe Baurens , Karine Labadie , Catherine Hervouet
Plant Journal, 2023, 113 (4), pp.802-818. ⟨10.1111/tpj.16086⟩
Journal articles hal-03992055v1
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Functional diversity of microbial eukaryotes in a meromictic lake: Coupling between metatranscriptomic and a trait‐based approach

Arthur Monjot , Gisèle Bronner , Damien Courtine , Corinne Cruaud , Corinne da Silva
Environmental Microbiology, inPress, ⟨10.1111/1462-2920.16531⟩
Journal articles hal-04273967v1
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Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Corentin Hochart , Lucas Paoli , Hans-Joachim Ruscheweyh , Guillem Salazar , Emilie Boissin
Nature Communications, 2023, 14 (1), pp.3037. ⟨10.1038/s41467-023-38502-9⟩
Journal articles hal-04176293v1
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Genome‐wide evolutionary response of European oaks during the Anthropocene

Dounia Saleh , Jun Chen , Jean-Charles Leplé , Thibault Leroy , Laura Truffaut
Evolution Letters, 2022, 6 (1), pp.4-20. ⟨10.1002/evl3.269⟩
Journal articles hal-03553889v1
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The genomic history and global expansion of domestic donkeys

Evelyn Todd , Laure Tonasso-Calvière , Loreleï Chauvey , Stéphanie Schiavinato , Antoine Fages
Science, 2022, 377 (6611), pp.1172-1180. ⟨10.1126/science.abo3503⟩
Journal articles hal-03827857v1
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The banana genome hub: a community database for genomics in the Musaceae

Gaëtan Droc , Guillaume Martin , Valentin Guignon , Marilyne Summo , Guilhem Sempéré
Horticulture research, 2022, 9, ⟨10.1093/hr/uhac221⟩
Journal articles hal-04361050v1
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Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

Jean-Marc Aury , Stefan Engelen , Benjamin Istace , Cécile Monat , Pauline Lasserre-Zuber
GigaScience, 2022, 11, pp.1-18. ⟨10.1093/gigascience/giac034⟩
Journal articles hal-03658639v1

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Tom Delmont , Morgan Gaia , Damien Hinsinger , Paul Frémont , Chiara Vanni
Cell Genomics, 2022, 2 (5), pp.100123. ⟨10.1016/j.xgen.2022.100123⟩
Journal articles hal-03872935v2
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Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France

Benoît Clavel , Sébastien Lepetz , Loreleï Chauvey , Stéphanie Schiavinato , Laure Tonasso-Calvière
Journal of Archaeological Science: Reports, 2022, 41, pp.103341. ⟨10.1016/j.jasrep.2022.103341⟩
Journal articles halshs-03755076v1

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

Ahmed Zayed , James Wainaina , Guillermo Dominguez-Huerta , Eric Pelletier , Jiarong Guo
Science, 2022, 376 (6589), pp.156-162. ⟨10.1126/science.abm5847⟩
Journal articles hal-03872940v1
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Gene expression and genetic divergence in oak species highlight adaptive genes to soil water constraints

Grégoire Le Provost , Benjamin Brachi , Isabelle Lesur , Céline Lalanne , Karine Labadie
Plant Physiology, 2022, 190 (4), pp.2466-2483. ⟨10.1093/plphys/kiac420/6692722⟩
Journal articles hal-03771214v1
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Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Daniel Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont
eLife, 2022, 11, pp.e78129. ⟨10.7554/eLife.78129⟩
Journal articles hal-02399723v2
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Transcriptome of the synganglion in the tick Ixodes ricinus and evolution of the cys-loop ligand-gated ion channel family in ticks

C. Rispe , Caroline Hervet , Nathalie de la Cotte , Romain Daveu , Karine Labadie
BMC Genomics, 2022, 23 (1), pp.1-20. ⟨10.1186/s12864-022-08669-4⟩
Journal articles hal-03707797v1
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Genomic adaptation of the picoeukaryote $Pelagomonas\ calceolata$ to iron-poor oceans revealed by a chromosome-scale genome sequence

Nina Guérin , Marta Ciccarella , Elisa Flamant , Paul Frémont , Sophie Mangenot
Communications Biology, 2022, 5 (1), pp.983. ⟨10.1038/s42003-022-03939-z⟩
Journal articles cea-03791710v1

Epigenomic and structural events preclude recombination in Brassica napus

Franz Boideau , Gautier Richard , Olivier Coriton , Virginie Huteau , Caroline Belser
New Phytologist, 2022, 234 (2), pp.545-559. ⟨10.1111/nph.18004⟩
Journal articles hal-03651949v1
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A Chromosome-level genome assembly of the European Beech (Fagus sylvatica) reveals anomalies for organelle DNA integration, repeat Content and distribution of SNPs

Bagdevi Mishra , Bartosz Ulaszewski , Joanna Meger , Jean-Marc Aury , Catherine Bodénès
Frontiers in Genetics, 2022, 12, pp.691058. ⟨10.3389/fgene.2021.691058⟩
Journal articles hal-03602006v1
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Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

Ahmed Zayed , James Wainaina , Guillermo Dominguez-Huerta , Eric Pelletier , Jiarong Guo
Science, 2022, 376 (6589), pp.156-162. ⟨10.1126/science.abm5847⟩
Journal articles hal-03781924v1
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Diversity and ecological footprint of Global Ocean RNA viruses

Guillermo Dominguez-Huerta , Ahmed Zayed , James Wainaina , Jiarong Guo , Funing Tian
Science, 2022, 376 (6598), pp.1202-1208. ⟨10.1126/science.abn6358⟩
Journal articles hal-03781935v1
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Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

Caroline Belser , Franc-Christophe Baurens , Benjamin Noel , Guillaume Martin , Corinne Cruaud
Communications Biology, 2021, 4 (1), ⟨10.1038/s42003-021-02559-3⟩
Journal articles hal-03352701v1
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Chromosome-scale assembly of the yellow mealworm genome

Evangelia Eleftheriou , Jean-Marc Aury , Benoît Vacherie , Benjamin Istace , Caroline Belser
Open Research Europe, 2021, 1, pp.94. ⟨10.12688/openreseurope.13987.3⟩
Journal articles hal-03770436v1
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Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

Jérémy Gauthier , Hélène Boulain , Joke J F A van Vugt , Lyam Baudry , Emma Persyn
Communications Biology, 2021, 4 (1), pp.1-15. ⟨10.1038/s42003-020-01623-8⟩
Journal articles hal-03127732v1
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Historical management of equine resources in France from the Iron Age to the Modern Period

Sébastien Lepetz , Benoît Clavel , Duha Alioğlu , Lorelei Chauvey , Stéphanie Schiavinato
Journal of Archaeological Science: Reports, 2021, 40 (B), pp.103250. ⟨10.1016/j.jasrep.2021.103250⟩
Journal articles hal-03431948v1
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Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

Jean-Marc Aury , Benjamin Istace
NAR Genomics and Bioinformatics, 2021, 3 (2), pp.lqab034. ⟨10.1093/nargab/lqab034⟩
Journal articles cea-04284756v1
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Population genomics of apricots unravels domestication history and adaptive events

Alexis Groppi , Shuo Liu , A. Cornille , David Tricon , Quynh Trang Bui
Nature Communications, 2021, 12 (1), pp.3956. ⟨10.1038/s41467-021-24283-6⟩
Journal articles hal-03282504v1
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Sequence diversity and evolution of a group of iflaviruses associated with ticks

Romain Daveu , Caroline Hervet , Louane Sigrist , Davide Sassera , Aaron Jex
Archives of Virology, 2021, 166 (7), pp.1843-1852. ⟨10.1007/s00705-021-05060-8⟩
Journal articles hal-03272097v1
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Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Laurence Garczarek , Ulysse Guyet , Hugo Doré , Gregory Farrant , Mark Hoebeke
Nucleic Acids Research, 2021, 49 (D1), pp.D667-D676. ⟨10.1093/nar/gkaa958⟩
Journal articles hal-02988562v1
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Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids

Pierre Clavel , Jean Dumoncel , Clio Der Sarkissian , Andaine Seguin-Orlando , Laure Calvière-Tonasso
Journal of Archaeological Science, 2021, 131, pp.105383. ⟨10.1016/j.jas.2021.105383⟩
Journal articles hal-03413040v1
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Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Diamantis Sellis , Frédéric Guérin , Olivier Arnaiz , Walker Pett , Emmanuelle Lerat
PLoS Biology, 2021, 19 (7), pp.e3001309. ⟨10.1371/journal.pbio.3001309⟩
Journal articles hal-03366429v1

Complete Genome Sequences of Two Pseudomonas Species Isolated from Marine Environments of the Pacific Ocean

Shi-Zhen Wang , Corinne Cruaud , Jean-Marc Aury , David Vallenet , Julie Poulain
Microbiology Resource Announcements, 2021, 10 (16), ⟨10.1128/mra.01062-19⟩
Journal articles hal-04178012v1
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The origins and spread of domestic horses from the Western Eurasian steppes

Pablo Librado , Naveed Khan , Antoine Fages , Mariya A Kusliy , Tomasz Suchan
Nature, 2021, 598 (7882), pp.634-640. ⟨10.1038/s41586-021-04018-9⟩
Journal articles hal-03425363v1
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Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Sarah Farhat , Phuong Le , Ehsan Kayal , Benjamin Noel , Estelle Bigeard
BMC Biology, 2021, 19 (1), ⟨10.1186/s12915-020-00927-9⟩
Journal articles hal-03114990v1
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Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Elise J Gay , Jessica L Soyer , Nicolas Lapalu , Juliette Linglin , Isabelle Fudal
BMC Biology, 2021, 19 (1), pp.e041118. ⟨10.1186/s12915-021-00989-3⟩
Journal articles hal-03190704v1
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Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

Benjamin Istace , Caroline Belser , Cyril Falentin , Karine Labadie , Franz Boideau
Biology, 2021, 10 (8), ⟨10.3390/biology10080732⟩
Journal articles hal-03318024v1
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BoardION: real-time monitoring of Oxford Nanopore sequencing instruments

Aimeric Bruno , Jean-Marc Aury , Stefan Engelen
BMC Bioinformatics, 2021, 22 (1), pp.e245. ⟨10.1186/s12859-021-04161-0⟩
Journal articles cea-04284759v1
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Virus-host coexistence in phytoplankton through the genomic lens

Sheree Yau , Marc Krasovec , L. Felipe Felipe Benites , Stéphane Rombauts , Mathieu Groussin
Science Advances , 2020, 6 (14), pp.eaay2587. ⟨10.1126/sciadv.aay2587⟩
Journal articles hal-02557501v1
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Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

Shinya Sato , Deepak Nanjappa , Richard G Dorrell , Fabio Rocha Jimenez Vieira , Elena Kazamia
Scientific Reports, 2020, 10 (1), pp.9449. ⟨10.1038/s41598-020-65941-x⟩
Journal articles inserm-02886223v1
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Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Hugo Doré , Gregory Farrant , Ulysse Guyet , Julie Haguait , Florian Humily
Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.567431⟩
Journal articles hal-02938656v1

Adaptive introgression as a driver of local adaptation to climate in European white oaks

Thibault Leroy , Jean-Marc Louvet , Céline Lalanne , Grégoire Le Provost , Karine Labadie
New Phytologist, 2020, 226 (4), pp.1171-1182. ⟨10.1111/nph.16095⟩
Journal articles hal-02627923v1
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Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa

Julien Boutte , Loeiz Maillet , Thomas Chaussepied , Sébastien Letort , Jean-Marc Aury
Frontiers in Plant Science, 2020, 11, pp.577536. ⟨10.3389/fpls.2020.577536⟩
Journal articles hal-03137565v1
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Long-read assembly of the Brassica napus reference genome Darmor-bzh

Mathieu Rousseau-Gueutin , Caroline Belser , Corinne Da silva , Gautier Richard , Benjamin Istace
GigaScience, 2020, 9 (12), pp.giaa137. ⟨10.1093/gigascience/giaa137⟩
Journal articles hal-03283975v1
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BiSCoT: improving large eukaryotic genome assemblies with optical maps

Benjamin Istace , Caroline Belser , Jean-Marc Aury
PeerJ, 2020, 8, pp.e10150. ⟨10.7717/peerj.10150⟩
Journal articles hal-04290135v1
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Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Luigi Caputi , Quentin Carradec , Damien Eveillard , Amos Kirilovsky , Eric Pelletier
Global Biogeochemical Cycles, 2019, 33 (3), pp.391-419. ⟨10.1029/2018GB006022⟩
Journal articles hal-02999805v1
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Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers

Thibault Leroy , Quentin Rougemont , Jean-Luc Dupouey , Catherine Bodenes , Céline Lalanne
New Phytologist, 2019, online fisrt, pp.1-15. ⟨10.1111/nph.16039⟩
Journal articles hal-02622295v1
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Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Julie Ferreira de Carvalho , Jérémy Lucas , Gwenaëlle Deniot , Cyril Falentin , Olivier Filangi
Plant Journal, 2019, 98 (3), pp.434-447. ⟨10.1111/tpj.14228⟩
Journal articles hal-02019346v1
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Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

Leandro Lima , Camille Marchet , Ségolène Caboche , Corinne da Silva , Benjamin Istace
Briefings in Bioinformatics, 2019, pp.1-18. ⟨10.1093/bib/bbz058⟩
Journal articles hal-02394395v1

A reference genome for pea provides insight into legume genome evolution

Jonathan J. Kreplak , Mohammed-Amin Madoui , Petr Cápal , Petr Novak , Karine Labadie
Nature Genetics, 2019, 51 (9), pp.1411-1422. ⟨10.1038/s41588-019-0480-1⟩
Journal articles hal-02278272v1
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The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean

Serge Planes , Denis Allemand , Sylvain Agostini , Bernard Banaigs , Emilie Boissin
PLoS Biology, 2019, 17 (9), pp.e3000483. ⟨10.1371/journal.pbio.3000483⟩
Journal articles hal-02402685v1
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Transposition favors the generation of large effect mutations that may facilitate rapid adaption

Leandro Quadrana , Mathilde Etcheverry , Arthur Gilly , Erwann Caillieux , Mohammed-Amin Madoui
Nature Communications, 2019, 10, ⟨10.1038/s41467-019-11385-5⟩
Journal articles hal-02398702v1
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The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

Lucas R Leclère , Coralie Horin , Sandra Chevalier , Pascal Lapébie , Philippe Dru
Nature Ecology & Evolution, 2019, 3 (5), pp.801-810. ⟨10.1038/s41559-019-0833-2⟩
Journal articles hal-02115215v1
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Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Camille Sessegolo , Corinne Cruaud , Corinne da Silva , Audric Cologne , Marion Dubarry
Scientific Reports, 2019, 9 (1), pp.14908. ⟨10.1038/s41598-019-51470-9⟩
Journal articles hal-02335574v1
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Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation

Elodie Gaulin , Michiel Pel , Laurent Camborde , Hélène San Clemente , Sarah Courbier
BMC Biology, 2018, 16 (1), ⟨10.1186/s12915-018-0508-5⟩
Journal articles hal-01891875v1

Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps

Caroline Belser , Benjamin Istace , Erwan Denis , Marion Dubarry , Franc-Christophe Baurens
Nature Plants, 2018, 4 (11), pp.879-887. ⟨10.1038/s41477-018-0289-4⟩
Journal articles hal-01977046v1
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Oak genome reveals facets of long lifespan

Christophe Plomion , Jean-Marc Aury , Joelle Amselem , Thibault Leroy , Florent Murat
Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩
Journal articles hal-01820559v1

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Rudi Appels , Kellye Eversole , Nils Stein , Catherine Feuillet , Beat Keller
Science, 2018, 361 (6403), ⟨10.1126/science.aar7191⟩
Journal articles hal-04331004v1
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Amphioxus functional genomics and the origins of vertebrate gene regulation

Ferdinand Marletaz , Panos N. Firbas , Ignacio Maeso , Juan J. Tena , Ozren Bogdanovic
Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩
Journal articles hal-02000511v1
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Hardwood tree genomics: unlocking woody plant biology

Gerald A. Tuskan , Andrew T. Groover , Jeremy Schmutz , Stephen Paul Difazio , Alexander Myburg
Frontiers in Plant Science, 2018, 9, pp.1-9. ⟨10.3389/fpls.2018.01799⟩
Journal articles hal-02622509v1
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A global ocean atlas of eukaryotic genes

Quentin Carradec , Eric Pelletier , Corinne da Silva , Adriana A. Alberti , Yoann Seeleuthner
Nature Communications, 2018, 9 (1), pp.373. ⟨10.1038/s41467-017-02342-1⟩
Journal articles cea-01874711v1
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De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

Fabien Dutreux , Corinne da Silva , Léo d'Agata , Arnaud Couloux , Elise Gay
Scientific Data , 2018, 5 (180235), 11 p. ⟨10.1038/sdata.2018.235⟩
Journal articles hal-02621276v1
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Complete genome sequence of the facultative methylotroph $Methylobacterium\ extorquens$ TK 0001 isolated from soil in Poland

Sophia Belkhelfa , Karine Labadie , Corinne Cruaud , Jean-Marc Aury , David Roche
Genome Announcements, 2018, 6 (8), ⟨10.1128/genomeA.00018-18⟩
Journal articles hal-04292575v1
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Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle

Claude Murat , Thibaut Payen , Benjamin Noël , Alan Kuo , Emmanuelle Morin
Nature Ecology & Evolution, 2018, 2 (12), pp.1956-1965. ⟨10.1038/s41559-018-0710-4⟩
Journal articles hal-02094494v1

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Rudi Appels , Kellye Eversole , Nils Stein , Catherine Feuillet , Beat Keller
Science, 2018, 361 (6403), ⟨10.1126/science.aar7191⟩
Journal articles hal-04198290v1
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De Novo Clustering of Long Reads by Gene from Transcriptomics Data

Camille Marchet , Lolita Lecompte , Corinne da Silva , Corinne Cruaud , Jean-Marc Aury
Nucleic Acids Research, inPress, pp.1-12. ⟨10.1093/nar/gky834⟩
Journal articles hal-01643156v2
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Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Amoebophrya Strains

Sarah Farhat , Isabelle Florent , Benjamin Noël , Ehsan Kayal , Corinne da Silva
Frontiers in Microbiology, 2018, 9, ⟨10.3389/fmicb.2018.02251⟩
Journal articles hal-02126891v1
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Genome evolution across 1,011 $Saccharomyces\ cerevisiae$ isolates

Jackson Peter , Matteo de Chiara , Anne Friedrich , Jia-Xing Yue , David Pflieger
Nature, 2018, 556 (7701), pp.339 - 344. ⟨10.1038/s41586-018-0030-5⟩
Journal articles cea-01872910v1
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Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Yoann Seeleuthner , Samuel Mondy , Vincent Lombard , Quentin Carradec , Eric Pelletier
Nature Communications, 2018, 9, pp.310. ⟨10.1038/s41467-017-02235-3⟩
Journal articles hal-01771839v1
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The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond , Jerome Gouzy , Jérémy Just , Hélène Badouin , Marion Verdenaud
Nature Genetics, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩
Journal articles hal-01798003v1
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Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Adriana A. Alberti , Julie Poulain , Stefan Engelen , Karine Labadie , Sarah Romac
Scientific Data , 2017, 4, ⟨10.1038/sdata.2017.93⟩
Journal articles hal-01771844v1
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Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes

Romain Blanc-Mathieu , Laetitia Zurletto , Jean-Marc Aury , Martine da Rocha , Jerome Gouzy
PLoS Genetics, 2017, 13 (6), pp.e1006777. ⟨10.1371/journal.pgen.1006777⟩
Journal articles hal-01602779v1
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High-quality $de\ novo$ genome assembly of the $Dekkera\ bruxellensis$ yeast using Nanopore MinION sequencing

Téo Fournier , Jean-Sébastien Gounot , Kelle Freel , Corinne Cruaud , Arnaud Lemainque
G3, 2017, 7 (10), pp.3243-3250. ⟨10.1534/g3.117.300128⟩
Journal articles cea-04315763v1
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$de\ novo$ assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

Benjamin Istace , Anne Friedrich , Léo d'Agata , Sébastien Faye , Emilie Payen
Gigascience, 2017, 6 (2), pp.giw018. ⟨10.1093/gigascience/giw018⟩
Journal articles cea-04315750v1
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Extensive recent secondary contacts between four European white oak species

Thibault Leroy , Camille Roux , Laure Villate , Catherine Bodénès , Jonathan Romiguier
New Phytologist, 2017, 214 (2), pp.865-878. ⟨10.1111/nph.14413⟩
Journal articles hal-01608621v1
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De novo assembly of a new Solanum pennellii accession using nanopore sequencing

Maximilian H.-W. Schmidt , Alexander Vogel , Alisandra K. Denton , Benjamin Istace , Alexandra Wormit
The Plant cell, 2017, 29, pp.2336-2348. ⟨10.1105/tpc.17.00521⟩
Journal articles hal-02625700v1

High-quality de novo genome assembly of the Dekkera bruxellensis yeast using Nanopore MinION sequencing

Téo Fournier , Jean-Sébastien Gounot , Kelle Freel , Corinne Cruaud , Arnaud Lemainque
G3, 2017, 7 (10), pp.3243-3250. ⟨10.1534/g3.117.300128⟩
Journal articles cea-04315747v1
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Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Anaïs Gouin , Anthony Bretaudeau , Kiwoong Nam , Sylvie Gimenez , Jean-Marc Aury
Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩
Journal articles hal-01633879v1
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The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies

Xavier Argout , Guillaume Martin , Gaetan Droc , Olivier Fouet , Karine Labadie
BMC Genomics, 2017, 18 (1), pp.730-739. ⟨10.1186/s12864-017-4120-9⟩
Journal articles lirmm-01612258v1
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Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).

Hélène Falentin , Stéphanie-Marie Deutsch , Valentin Loux , Amal Hammani , Julien Buratti
Standards in Genomic Sciences, 2016, 11, pp.6. ⟨10.1186/s40793-015-0120-z⟩
Journal articles hal-02640172v1
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Survey of the green picoalga Bathycoccus genomes in the global ocean

Thomas Vannier , Jade Leconte , Yoann Seeleuthner , Samuel Mondy , Eric Pelletier
Scientific Reports, 2016, 6, pp.37900. ⟨10.1038/srep37900⟩
Journal articles hal-01410203v1
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A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

Rafael Acemel , Juan Tena , Ibai Irastorza-Azcarate , Ferdinand Marlétaz , Carlos Gómez-Marín
Nature Genetics, 2016, 48 (3), pp.336-341. ⟨10.1038/ng.3497⟩
Journal articles hal-03881440v1
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MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

Mohammed-Amin Madoui , Carole Dossat , Léo D’agata , Jan van Oeveren , Edwin van der Vossen
BMC Bioinformatics, 2016, 17 (1), pp.115. ⟨10.1186/s12859-016-0969-x⟩
Journal articles hal-04535098v1

Implication of the suberin pathway in adaptation to waterlogging and hypertrophied lenticels formation in pedunculate oak (Quercus robur L.)

Grégoire Le Provost , Isabelle Lesur Kupin , Céline Lalanne , Corinne da Silva , Karine Labadie
Tree Physiology, 2016, 36 (11), pp.1330-1342. ⟨10.1093/treephys/tpw056⟩
Journal articles hal-01602423v1
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Genome assembly using Nanopore-guided long and error-free DNA reads

Mohammed-Amin Madoui , Stefan Engelen , Corinne Cruaud , Caroline Belser , Laurie Bertrand
BMC Genomics, 2015, 16 (1), pp.327. ⟨10.1186/s12864-015-1519-z⟩
Journal articles hal-04361027v1
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Eukaryotic plankton diversity in the sunlit ocean

Noan Le Bescot , Ian Probert , Margaux Carmichael , Julie Poulain , Sarah Romac
Science, 2015, 348 (6237), pp.1261605. ⟨10.1126/science.1261605⟩
Journal articles hal-01253979v1
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Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

Valentin Loux , Mahendra Mariadassou , Sintia Almeida , Hélène Chiapello , Amal Hammani
BMC Genomics, 2015, 16 (1), pp.35. ⟨10.1186/s12864-015-1467-7⟩
Journal articles hal-01142363v1
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Recurrent domestication by Lepidoptera of genes from their parasites mediated by Bracoviruses

Laila Gasmi , Hélène Boulain , Jérémy Gauthier , Aurélie Hua-Van , Karine Musset
PLoS Genetics, 2015, 11 (9), 32 p. ⟨10.1371/journal.pgen.1005470⟩
Journal articles hal-01220732v1
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Recurrent DNA virus domestication leading to different parasite virulence strategies

Apolline Pichon , Annie Bézier , Serge Urbach , Jean-Marc Aury , Véronique Jouan
Science Advances , 2015, 1 (10), pp.e1501150. ⟨10.1126/sciadv.1501150⟩
Journal articles hal-01318262v1
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The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Isabelle Lesur , Grégoire G. Le Provost , Pascal Bento , Corinne da Silva , Jean-Charles Leplé
BMC Genomics, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩
Journal articles hal-02285504v1

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

Christophe Plomion , Jean-Marc Aury , Joëlle Amselem , Tina Alaeitabar , Valérie Barbe
Molecular Ecology Resources, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩
Journal articles hal-01579667v1
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Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?

Pascaline Dumas , Fabrice Legeai , Claire Lemaitre , Erwan Scaon , Marion Orsucci
Genetica, 2015, 143 (3), pp.305-316. ⟨10.1007/s10709-015-9829-2⟩
Journal articles hal-01208780v2
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The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

Betina M Porcel , France Denoeud , Fred Opperdoes , Benjamin Noel , Mohammed-Amine Madoui
PLoS Genetics, 2014, 10 (2), pp.e1004007. ⟨10.1371/journal.pgen.1004007⟩
Journal articles hal-04402160v1
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TE-Tracker: systematic identification of transposition events through whole-genome resequencing

Arthur Gilly , Mathilde Etcheverry , Mohammed-Amin Madoui , Julie Guy , Leandro Quadrana
BMC Bioinformatics, 2014, 15 (1), ⟨10.1186/s12859-014-0377-z⟩
Journal articles hal-03170927v1

Mapping the epigenetic basis of complex traits

Sandra Cortijo , Rene Wardenaar , Maria Colomé-Tatché , Arthur Gilly , Mathilde Etcheverry
Science, 2014, 343 (6175), pp.1145-1148. ⟨10.1126/science.1248127⟩
Journal articles hal-01193838v1
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A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp.

Sophia S. Ahmed , J. Mark Cock , Eugenie Pessia , Remy Luthringer , Alexandre Cormier
Current Biology - CB, 2014, 24 (17), pp.1945-1957. ⟨10.1016/j.cub.2014.07.042⟩
Journal articles hal-01132642v1
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Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus

Florian Humily , Gregory K. Farrant , Dominique Marie , Frédéric Partensky , Sophie Mazard
FEMS Microbiology Ecology, 2014, 88 (2), pp.231-249. ⟨10.1111/1574-6941.12285⟩
Journal articles hal-01100993v1
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Structural and Functional Partitioning of Bread Wheat Chromosome 3B

Frédéric Choulet , Adriana A. Alberti , Sébastien Theil , Natasha Marie Glover , Valérie Barbe
Science, 2014, 345 (6194), ⟨10.1126/science.1249721⟩
Journal articles hal-02638189v1

Genome-defence small RNAs exapted for epigenetic mating-type inheritance.

Deepankar Pratap Singh , Baptiste Saudemont , Gérard Guglielmi , Olivier Arnaiz , Jean-François Goût
Nature, 2014, 509 (7501), pp.447-52. ⟨10.1038/nature13318⟩
Journal articles hal-01015302v1
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The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

France Denoeud , Lorenzo Carretero-Paulet , Alexis Dereeper , Gaëtan Droc , Romain Guyot
Science, 2014, 345 (6201), pp.1181-1184. ⟨10.1126/science.1255274⟩
Journal articles hal-02641562v1
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Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

Adriana A. Alberti , Caroline Belser , Stefan Engelen , Laurie Bertrand , Celine Orvain
BMC Genomics, 2014, 15, pp.912. ⟨10.1186/1471-2164-15-912⟩
Journal articles hal-02503091v1

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Boulos Chalhoub , France Denoeud , Shengyi Liu , Isobel A. P. Parkin , Haibao Tang
Science, 2014, 345 (6199), pp.950-953. ⟨10.1126/science.1253435⟩
Journal articles hal-01208705v1
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The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.

Camille Berthelot , Frédéric Brunet , Domitille Chalopin , Amélie Juanchich , Maria Bernard
Nature Communications, 2014, 5, pp.1-10. ⟨10.1038/ncomms4657⟩
Journal articles hal-01193812v1
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Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.

Jonas Collén , Betina Porcel , Wilfrid Carré , Steven G Ball , Cristian Chaparro
Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (13), pp.5247-52. ⟨10.1073/pnas.1221259110⟩
Journal articles hal-01073830v1
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Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

Jean-François Flot , Boris Hespeels , Xiang Li , Benjamin Noel , Irina Arkhipova
Nature, 2013, 500 (7463), pp.453-457. ⟨10.1038/nature12326⟩
Journal articles hal-01282538v1

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.

Olivier Arnaiz , Nathalie Mathy , Céline Baudry , Sophie Malinsky , Jean-Marc Aury
PLoS Genetics, 2012, 8 (10), pp.e1002984. ⟨10.1371/journal.pgen.1002984⟩
Journal articles hal-00759182v1

The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium

J. Mark Cock , Lieven Sterck , Sophia Ahmed , Andrew E. Allen , Grigoris Amoutzias
Advances in Botanical Research, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩
Journal articles hal-02649287v1

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

Angélique d'Hont , France Denoeud , Jean-Marc Aury , Franc-Christophe Baurens , Françoise Carreel
Nature, 2012, 488 (7410), pp.213-7. ⟨10.1038/nature11241⟩
Journal articles hal-00855582v1
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In Silico Survey of the Mitochondrial Protein Uptake and Maturation Systems in the Brown Alga Ectocarpus siliculosus

Ludovic Delage , Catherine Leblanc , Pi Nyvall Collén , Bernhard Gschloessl , Marie-Pierre Oudot
PLoS ONE, 2011, 6 (5), pp.e19540. ⟨10.1371/journal.pone.0019540⟩
Journal articles hal-01806425v1
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Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite.

France Denoeud , Michaël Roussel , Benjamin Noel , Ivan Wawrzyniak , Corinne da Silva
Genome Biology, 2011, 12 (3), pp.R29. ⟨10.1186/gb-2011-12-3-r29⟩
Journal articles inserm-00617212v1

The genome of Theobroma cacao.

Xavier Argout , Jerome Salse , Jean-Marc Aury , Mark J Guiltinan , Gaetan Droc
Nature Genetics, 2011, 43 (2), pp.101-8. ⟨10.1038/ng.736⟩
Journal articles hal-00855922v1
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Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

Francis Martin , Annegret Kohler , Claude Murat , Raffaella Balestrini , Pedro M Coutinho
Nature, 2010, 464 (7291), pp.1033-1038. ⟨10.1038/nature08867⟩
Journal articles cea-00907731v1
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Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

France Denoeud , Simon Henriet , Sutada Mungpakdee , Jean-Marc Aury , Corinne da Silva
Science, 2010, 330 (6009), pp.1381-1385. ⟨10.1126/science.1194167⟩
Journal articles halsde-00544648v1
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The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae

J. Mark Cock , Lieven Sterck , Pierre Rouzé , Delphine Scornet , Andrew E. Allen
Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩
Journal articles cea-00906990v1

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline

L. Duret , J. Cohen , C. Jubin , P. Dessen , J.-F. Gout
Genome Research, 2008, 18, pp.585-596. ⟨10.1101/gr.074534.107⟩
Journal articles hal-00428190v1

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline.

L. Duret , Jean Cohen , Claire Jubin , Philippe Dessen , Jean-François Goût
Genome Research, 2008, 18 (4), pp.585-96. ⟨10.1101/gr.074534.107⟩
Journal articles hal-00282468v1
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Annotating genomes with massive-scale RNA sequencing

France Denoeud , Jean-Marc Aury , Corinne da Silva , Benjamin Noel , Odile Rogier
Genome Biology, 2008, 9 (12), ⟨10.1186/gb-2008-9-12-r175⟩
Journal articles hal-02664963v1

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Pierre Abad , Jerome Gouzy , Jean-Marc Aury , Philippe Castagnone-Sereno , Etienne Danchin
Nature Biotechnology, 2008, 26 (8), pp.909-915. ⟨10.1038/nbt.1482⟩
Journal articles hal-01189285v1
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High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

Jean-Marc Aury , Corinne Cruaud , Valérie Barbe , Odile Rogier , Sophie Mangenot
BMC Genomics, 2008, 9, ⟨10.1186/1471-2164-9-603⟩
Journal articles hal-02659381v1
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The genome sequence of the model ascomycete fungus Podospora anserina.

Eric Espagne , Olivier Lespinet , Fabienne Malagnac , Corinne da Silva , Olivier Jaillon
Genome Biology, 2008, 9 (5), pp.R77. ⟨10.1186/gb-2008-9-5-r77⟩
Journal articles hal-00286300v1

The genome sequence of the model ascomycete fungus Podospora anserina

Eric Espagne , Olivier Lespinet , Fabienne Malagnac , Corinne da Silva , Olivier Jaillon
Genome Biology, 2008, 9 (5), pp.R77. ⟨10.1186/gb-2008-9-5-r77⟩
Journal articles hal-04011226v1
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Translational control of intron splicing in eukaryotes

Olivier Jaillon , Khaled Bouhouche , Jean-François Gout , Jean-Marc Aury , Benjamin Noel
Nature, 2008, 451 (7176), pp.359-362. ⟨10.1038/nature06495⟩
Journal articles cea-00945555v1
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The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Olivier Jaillon , Jean-Marc Aury , Benjamin Noel , Alberto Policriti , Christian Clepet
Nature, 2007, 449 (7161), pp.463-7. ⟨10.1038/nature06148⟩
Journal articles inria-00180136v1

Global trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia

Jean-Marc Aury , Olivier Jaillon , * Laurent Duret , Benjamin Noel , Claire Jubin
Nature, 2006, 444 (7116), pp.171-178. ⟨10.1038/nature05230⟩
Journal articles hal-00090904v1

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

Frédéric Brunet , Hugues Roest Crollius , Mathilde Paris , Jean-Marc Aury , Patricia Gibert
Molecular Biology and Evolution, 2006, 23 (9), pp.1808-1816. ⟨10.1093/molbev/msl049⟩
Journal articles hal-02660787v1

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

Jean-Marc Aury , Olivier Jaillon , L. Duret , Benjamin Noel , Claire Jubin
Nature, 2006, 444 (7116), pp.171-8. ⟨10.1038/nature05230⟩
Journal articles hal-00132091v1

Genome duplication in the teleost fish Tretraodon nigroviridis reveals the early vertebrate proto-karyotype

Olivier Jaillon , J.M. Aury , F. Brunet , J.L. Petit , N. Stange-Thomann
Nature, 2004, 431, pp.946-957
Journal articles hal-02681415v1

Whole genome sequence comparisons and "full-lenght" cDNA sequences: a combined approach to evaluate and improve Arabidopdid genome annotation

V. Castelli , J.M. Aury , Olivier Jaillon , Patrick Wincker , Christian Clepet
Genome Research, 2004, 14 (3), pp.406-413
Journal articles hal-02672600v1

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

O. Jaillon , J.-M. Aury , F. Brunet , J.L. Petit , N. Stange-Thomann
Nature, 2004, 431, pp.946-957. ⟨10.1038/nature03025⟩
Journal articles hal-00427605v1

Deciphering metatranscriptomic data

Evguenia Kopylova , Laurent Noé , Corinne da Silva , Jean-Frédéric Berthelot , Adriana A. Alberti
Methods in Molecular Biology, 1269, Springer, pp.279-291, 2015, RNA Bioinformatics, 978-1-4939-2290-1. ⟨10.1007/978-1-4939-2291-8_17⟩
Book sections hal-01104015v1

De novo sequencing and assembly of genomes using long reads

Jean-Marc Aury
Revolutionizing Next-Generation Sequencing, Mar 2023, Ghent, Belgium
Conference papers hal-04443667v1
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European mink (Mustela lutreola) reference genome and population genomics

Alice Mouton , Christine Fournier-Chambrillon , Pascal Fournier , Jakub Skorupski , Przemysław Śmietana
34th European Mustelid Colloquium, Sep 2022, Online conference, France
Conference papers hal-03787589v1

De novo sequencing and assembly of complex genomes

Jean-Marc Aury
reads2genpop : From sequence reads to genomes and populations, Sep 2022, Paris, Auditorium de la Grande Galerie de l’Evolution, France
Conference papers hal-04443758v1

High-quality genome assemblies of corals highlight the specifics of their long lifespan

France Denoeud , Benjamin Noel , Julie Poulain , Carol Bruitago , Quentin Carradec
EAGS, France Génomique, Oct 2021, Tours (France), France
Conference papers hal-04440766v1

De novo sequencing and assembly of complex genomes

Jean-Marc Aury
Environmental and Agronomical Genomics Symposium, Oct 2021, Tours, France
Conference papers hal-04443602v1

Avancées sur l’amélioration de l’assemblage de la variété de colza Darmor via l’utilisation des dernières technologies de séquençage

Mathieu Rousseau-Gueutin , Jean-Marc Aury
26e Carrefour de la sélection du colza, Jan 2020, Orléans, France
Conference papers hal-03318169v1

Co-evolution of chloroplast and nuclear genomes in flowering plants and impact of allopolyploidy on fine tune cytonuclear interactions.

Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , Jérémy Lucas , Gwenaëlle Deniot , Cyril Falentin
International Conference on Polyploidy, Jun 2019, Ghent, Belgium
Conference papers hal-03318182v1

Chromosome-Scale Assemblies of Plant Genomes using Nanopore Long Reads and Optical Maps

Jean-Marc Aury
Plant and Animal Genome XXVII Conference, Jan 2019, San Diego, United States
Conference papers hal-04443565v1

Pelagia noctiluca as a model to uncover scyphozoan developmental mechanisms.

Y. Kraus , R. Copley , J.M. Aury , F. Rentzsch , F. Lombard
At the roots of bilaterian complexity: Insights from early emerging metazoans., 2019, Evangelische Akademie Tutzing, Germany
Conference papers hal-04024044v1

Structural and functional evolutionary dynamics of duplicated genes and genomes in nascent and natural B. napus

Mathieu Rousseau-Gueutin , Jérémy Lucas , France Denoeud , Julie Ferreira de Carvalho , Zhesi He
21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2019, Saint-Malo, France
Conference papers hal-03318226v1

Deciphering the synganglion transcriptome of Ixodes ricinus

Claude Rispe , Caroline Hervet , Jean-Marc Aury , Karine Labadie , Steeve Thany
14. Réunion annuelle du groupe « Tiques et Maladies Transmises » du « Réseau Ecologie Interactions Durable » (REID), May 2019, Montpellier, France
Conference papers hal-02786923v1
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CARNAC-LR : Clustering coefficient-based Acquisition of RNA Communities in Long Reads

Camille Marchet , Lolita Lecompte , Corinne da Silva , Corinne Cruaud , Jean-Marc Aury
JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. pp.1-3
Conference papers hal-01930211v1

How a polyploid becomes a new species: example from the Brassica model.

Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , J. Lucas , France Denoeud , Fabrice Legeai
International Conference on Environmental and Agronomical Genomics, 2018, Paris, France
Conference papers hal-03318223v1
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An integrated information system dedicated to oak genomics and genetics

Joëlle Amselem , Nicolas Francillonne , Célia Michotey , Thomas Letellier , Jean-Marc Aury
PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides
Conference papers hal-01839185v1

Cytonuclear interactions overcome inter-genomic conflict resulting from interspecific hybridization and genome doubling

Julie Ferreira de Carvalho , Jérémy Lucas , Cyril Falentin , Gwenaëlle Deniot , Olivier Filangi
Second Joint Congress on Evolutionary Biology, Aug 2018, Montpellier, France
Conference papers hal-03318235v1
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Identification et analyse fonctionnelle des effecteurs tardifs impliqués dans la colonisation systémique du colza par Leptosphaeria maculans

Julie Gervais , Elise Gay , Fabien Dutreux , Isabelle Fudal , Juliette Linglin
Journées Jean Chevauchon JJC2018 - 12èmes Rencontres de Phytopathologie & Mycologie,, Jan 2018, Aussois, France. p.50
Conference papers hal-02786060v1

Discovering genes involved in ecological preference in European white oaks using an RNAseq approach

Grégoire Le Provost , Isabelle Lesur , Céline Lalanne , Karine Labadie , Jean Marc Aury
Workshop on Fagaceae and Nothofagaceae genetics and genomics, Nov 2017, Shangai, China
Conference papers hal-03351960v1

Identification of recent secondary contacts between four morphologically distinct oak species

Thibault Leroy , Camille Roux , Catherine Bodenes-Brezard Bodénès , Jean-Marc Aury , Antoine Kremer
Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p
Conference papers hal-02743580v1

Annotation of the oak genome sequence and associated bioinformatic resources

Joelle J. Amselem , Jean Marc Aury , Nicolas Francillonne , Tina Alaeitabar , Corinne da Silva
IUFRO Genomics and Forest Tree Genetics, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p
Conference papers hal-02741128v1

Discovering genes involved in ecological speciation in European white oaks using an RNAseq approach

Grégoire G. Le Provost , Isabelle Lesur Kupin Lesur , Céline C. Lalanne , Karine Labadie , Jean Marc Aury
Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p
Conference papers hal-02741267v1

Oak genome sequencing and evolution

Jerome J. Salse , Jean Marc Aury , Florent Murat , Sébastien Faye , Karine Labadie
Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p
Conference papers hal-02741698v1

Recurrent domestication of viral genomes leads to different virulence strategies in ichneumonid wasps

Jean Marc Aury , Valérie Barbe , Annie Bezier , Jean-Michel Drezen , Véronique Jouan
Réunion du réseau ADALEP, 2016, Paris, France
Conference papers hal-01991475v1

Using genomic tools to unravel parasitic wasp genome evolution via acquisition of viral genomes

Anne-Nathalie Volkoff , Jean-Michel Drezen , Serge Urbach , Apolline Pichon , Véronique Jouan
Arthropod Genomics Symposium, 2015, Manhattan, Kansas, United States
Conference papers hal-01991470v1
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Assembling a pseudomolecule for a wheat chromosome: the 3B experience

Frédéric Choulet , Adriana A. Alberti , Valérie Barbe , Sébastien Theil , Pierre Sourdille
22. Conference on Plant and Animal Genome, Jan 2014, San Diego, Californie, United States
Conference papers hal-02743902v1

Origine évolutive des “Virus-like particles” de Venturia canescens

Apolline Pichon , Serge Urbach , Jean Marc Aury , Annie Bezier , Véronique Jouan
Réunion annuelle du Réseau Ecologie des Interactions Durables (REID), Feb 2014, Montpellier, France
Conference papers hal-01991483v1

Acquisition of viruses as a driver in endoparasitic ichneumonid wasp evolution

Apolline Pichon , Serge Urbach , Annie Bezier , Jean Marc Aury , Véronique Jouan
CNRS Jacques Monod Conference "Infectious diseases as drivers of evolution: the challenges ahead”, 2014, Roscoff, France
Conference papers hal-01991478v1
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Sequencing and Assembling a Reference Sequence of the 1 Gb Wheat Chromosome 3B

Frédéric Choulet , Sébastien Theil , Josquin Daron , Natasha Marie Glover , Nicolas N. Guilhot
IWGSC Wheat Genome Sequencing Strategy and Funding Workshop, International Wheat Genome Sequencing Consortium (IWGSC). USA., Apr 2013, Evry, France
Conference papers hal-02747374v1

Sequencing and analysis of the oak transcriptome using RNA-seq technologies

Isabelle Lesur Kupin Lesur , Grégoire G. Le Provost , Céline C. Lalanne , François Ehrenmann , Céline Noirot
IUFRO working group “Genetics of Quercus and Nothofagus”, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p
Conference papers hal-02806071v1

Genomic resources for functional analysis in Medicago truncatula and related crop species

Frederic Debellé , C. Belser , J.M. Aury , K. Labadie , Brice Roux
6. International Conference on Legume Genetics and Genomics, International Crops Research Institute for the Semi-Arid Tropics, CGIAR (ICRISAT). Patancheru, IND., Oct 2012, Hyderabad, India
Conference papers hal-02747944v1
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A strategy to assemble a reference sequence of the 1 Gb wheat chromosome 3B

Frédéric Choulet , Sébastien Theil , Josquin Daron , Natasha Marie Glover , Nicolas N. Guilhot
TGAC/ESF-LESC workshop, Strategies for de novo assemblies of complex crop genomes, Genome Analysis Centre (TGAC). Norwich, GBR., Oct 2012, Norwich, United Kingdom
Conference papers hal-02809032v1

Development of genomic resources to study the structure, function and evolution of the oak genome

Christophe Plomion , Joelle J. Amselem , Jean-Marc Aury , Catherine Bodenes , Emilie Chancerel
IUFRO working group "Genetics of Quercus and Nothofagus", Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p
Conference papers hal-01019850v1

Nature, nurture and the structure of macroalgal genomes

J. Mark Cock , Jonas Collen , Lieven Sterck , Pierre Rouzé , Delphine Scornet
5. European Phycological Congress, Sep 2011, Rhodes, Greece
Conference papers hal-02749757v1