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Caroline Menguy

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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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Diversity of the Pacific Ocean coral reef microbiome

Pierre Galand , Hans-Joachim Ruscheweyh , Guillem Salazar , Corentin Hochart , Nicolas Henry
Nature Communications, 2023, 14 (1), pp.3039. ⟨10.1038/s41467-023-38500-x⟩
Journal articles hal-04176291v1

Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments

Blandine Trouche , Clemens Schauberger , Feriel Bouderka , Jean-Christophe Auguet , Caroline Belser
ISME Communications, 2023, 3 (1), pp.133. ⟨10.1038/s43705-023-00341-6⟩
Journal articles hal-04388214v1
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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
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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

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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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
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Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection

Aurélie Canaguier , Romane Guilbaud , Erwan Denis , Ghislaine Magdelenat , Caroline Belser
BMC Genomics, 2022, 23 (1), pp.317. ⟨10.1186/s12864-022-08499-4⟩
Journal articles hal-03977388v1

Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans

Naama Lang-Yona , J. Michel Flores , Rotem Haviv , Adriana Alberti , Julie Poulain
Communications Earth & Environment, 2022, 3 (1), pp.121. ⟨10.1038/s43247-022-00441-6⟩
Journal articles hal-04382382v1
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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
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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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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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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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Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

Miriam I Brandt , Florence Pradillon , Blandine Trouche , Nicolas Henry , Cathy Liautard-Haag
Scientific Reports, 2021, 11 (1), pp.7856. ⟨10.1038/s41598-021-86396-8⟩
Journal articles hal-03198097v1
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Diversity and biogeography of bathyal and abyssal seafloor bacteria and archaea along a Mediterranean-Atlantic gradient

Blandine Trouche , Miriam Brandt , Caroline Belser , Covadonga Orejas , Stephane Pesant
Frontiers in Microbiology, 2021, 12, pp.702016. ⟨10.3389/fmicb.2021.702016⟩
Journal articles hal-03589735v1
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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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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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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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Draft Genome Sequence of Tubulinosema ratisbonensis , a Microsporidian Species Infecting the Model Organism Drosophila melanogaster

Valérie Polonais , Sebastian Niehus , Ivan Wawrzyniak , Adrien Franchet , Christine Gaspin
Microbiology Resource Announcements, 2019, 8 (31), ⟨10.1128/MRA.00077-19⟩
Journal articles hal-02276377v1
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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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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

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

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
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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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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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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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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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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

The DNA sequence and analysis of human chromosome 14

Roland Heilig , Ralph Eckenberg , Jean-Louis Petit , Núria Fonknechten , Corinne da Silva
Nature, 2003, 421 (6923), pp.601-607. ⟨10.1038/nature01348⟩
Journal articles hal-04312826v1
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LONG DNA TECHNOLOGIES EVALUATION FOR PLANT STRUCTURAL VARIATIONS DETECTION : NANOPORE ONT SEQUENCING vs BIONANO GENOMICS OPTICAL MAPPING

Aurélie Canaguier , Erwan Denis , Romane Guilbaud , Ghislaine Magdelenat , Caroline Belser
Plant and Animal Genome XXVIII Conference, Jan 2020, San Diego, United States.
Conference poster hal-02925940v1

Long DNA technologies evaluation for plant structural variations detection: Nanopore ONT sequencing vs Bionano Genomics optical mapping

Aurélie Canaguier , Erwan Denis , Romane Guilbaud , Ghislaine Magdelenat , Caroline Belser
- Plant and Animal Genome XXVIII Conference, 2020, San Diego, CA, United States
Conference poster hal-04331757v1

Chromosome-scale assemblies of Brassica oleracea and Brassica rapa using nanopore long reads and optical maps

Caroline Belser , Bejamin Istace , Denis Engemann , M Dubarry , Cyril Falentin
21st Crucifer Genetics Conference on Brassica - Bassica 2018, Jul 2018, Saint-Malo, France
Conference poster hal-03318378v1

Optical Mapping with the Saphyr System on Plant Genomes

Erwan Denis , Caroline Belser , Wahiba Berrabah , Ghislaine Magdelenat , Corinne Cruaud
- Plant and Animal Genome XXVI Conference, 2018, San Diego (CA), United States
Conference poster hal-04331771v1

From whole-genome scans for divergence to the discovery of speciation genes in oaks

Thibault Leroy , Jean Marc Aury , Catherine Bodenes-Brezard Bodénès , Laure Villate , Grégoire G. Le Provost
15. Congress of the European Society for Evolutionary Biology (ESEB), Aug 2015, Lausanne, Switzerland. , 1 p., 2015
Conference poster hal-02797182v1
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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

The Pisum Genus: Getting out of Pea Soup!

Jonathan Kreplak , Mohammed-Amin Madoui , Karine Labadie , Grégoire Aubert , Petr Capal
Plant and Animal Genome XXVI Conference, 2018, San Diego (CA), United States
Conference papers hal-04331722v1
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The pea genome

Jonathan Kreplak , Mohammed-Amin Madoui , Karine Labadie , Gregoire Aubert , Philippe Bayer
8. International Conference on Legume Genetics and Genomics (ICLGG), Noble Research Institute., Sep 2017, Siófok, Hungary. 128 p
Conference papers hal-02735156v1
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Towards the genome sequence of pea : a tribute to Mendel

Mohammed-Amin Madoui , K. Labadie , Jonathan Kreplak , Gregoire Aubert , Léo d'Agata
2. International Legume Society Conference - Legumes for a Sustainable World, Legume Society., Oct 2016, Lisbone, Portugal. 358 p
Conference papers hal-01602206v1

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

TARA Pacific CTAX colony morphological annotations release version 1_1

Guinther Mitushasi , Sylvain Algostini , Benjamin Hume , Yuko Kitano , Julie Poulain
Other publications hal-04384090v1

TARA Pacific bleaching prevalence of sampling sites (Islands)

Christian R Voolstra , Benjamin C.C Hume , Kyra Pikaar , Guillaume Bourdin , Stéphane Pesant
Other publications hal-04384087v1

Tara Pacific V9 18S rDNA metabarcoding dataset

Frédéric Mahé , Nicolas Henry , Cédric Berney , Julie Poulain , Sarah Romac
Other publications hal-04384095v1

Tara Pacific metabarcoding sequencing (16S, 18S, ITS2) reference & replication tables version 1

Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh
Other publications hal-04384100v1

Tara Pacific 16S rRNA data analysis release

Hans-Joachim Ruscheweyh , Guillem Salazar , Julie Poulain , Caroline Belser , Quentin Clayssen
Other publications hal-04384109v1

Tara Pacific ITS2 Symbiodiniaceae data release version 1

Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh
Other publications hal-04384112v1

Tara Pacific 18S-based coral host genetic analysis data release version 1

Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh
Other publications hal-04384097v1
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Approches bioinformatiques pour l'exploration des génomes et de la biodiversité

Caroline Belser
Génomique, Transcriptomique et Protéomique [q-bio.GN]. Université Paris-Saclay, 2022. Français. ⟨NNT : 2022UPASB073⟩
Theses tel-03994054v1