Caroline Menguy

Documents

Publications

	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⟩ Article dans une revue hal-04489824v1
	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⟩ Article dans une revue hal-04176297v1
	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⟩ Article dans une revue hal-04388214v1
	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⟩ Article dans une revue hal-04176291v1
	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⟩ Article dans une revue cea-04171796v1
	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⟩ Article dans une revue 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⟩ Article dans une revue hal-03651949v1
	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⟩ Article dans une revue hal-03977388v1
	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⟩ Article dans une revue hal-03658639v1
	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⟩ Article dans une revue hal-04382382v1
	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⟩ Article dans une revue hal-03198097v1
	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⟩ Article dans une revue hal-03352701v1
	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⟩ Article dans une revue hal-03770436v1
	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⟩ Article dans une revue hal-03318024v1
	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⟩ Article dans une revue hal-03589735v1
	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⟩ Article dans une revue hal-03282504v1
	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⟩ Article dans une revue hal-03283975v1
	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⟩ Article dans une revue hal-04290135v1
	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⟩ Article dans une revue hal-03137565v1
	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⟩ Article dans une revue hal-02622295v1
	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⟩ Article dans une revue hal-02276377v1
	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⟩ Article dans une revue 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⟩ Article dans une revue 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⟩ Article dans une revue hal-01977046v1
	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⟩ Article dans une revue hal-01820559v1
	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⟩ Article dans une revue hal-01771844v1
	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⟩ Article dans une revue hal-01633879v1
	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⟩ Article dans une revue hal-04361027v1
	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⟩ Article dans une revue 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⟩ Article dans une revue hal-01579667v1
	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⟩ Article dans une revue 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⟩ Article dans une revue hal-04312826v1

	TARA Pacific CTAX colony morphological annotations release version 1_1 Guinther Mitushasi , Sylvain Algostini , Benjamin Hume , Yuko Kitano , Julie Poulain 2022, ⟨10.5281/zenodo.6384774⟩ Autre publication scientifique hal-04384090v1
	TARA Pacific Bleaching Prevalence of Sampling Sites (Islands) Kyra Pikaar , Guillaume Bourdin , Stéphane Pesant , Julie Poulain , Caroline Belser 2022, ⟨10.5281/zenodo.6511406⟩ Autre publication scientifique hal-04384087v1
	Tara Pacific V9 18S rDNA metabarcoding dataset Frédéric Mahé , Nicolas Henry , Cédric Berney , Julie Poulain , Sarah Romac 2021, ⟨10.5281/zenodo.5041070⟩ Autre publication scientifique 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 2020, ⟨10.5281/ZENODO.4073035⟩ Autre publication scientifique hal-04384100v1
	Tara Pacific 16S rRNA data analysis release Hans-Joachim Ruscheweyh , Guillem Salazar , Julie Poulain , Caroline Belser , Quentin Clayssen 2020, ⟨10.5281/ZENODO.4073269⟩ Autre publication scientifique hal-04384109v1
	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 2020, ⟨10.5281/zenodo.4265266⟩ Autre publication scientifique hal-04384097v1
	Tara Pacific ITS2 Symbiodiniaceae data release version 1 Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh 2020, ⟨10.5281/zenodo.4061797⟩ Autre publication scientifique hal-04384112v1

	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 Communication dans un congrès 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 Communication dans un congrès hal-04331722v1
	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 Communication dans un congrès hal-02735156v1
	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 Communication dans un congrès 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 Communication dans un congrès hal-02747944v1

	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⟩ Thèse tel-03994054v1

	The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics Ann M Mc Cartney , Giulio Formenti , Alice Mouton , Diego de Panis , Luísa S Marins 2024 Pré-publication, Document de travail hal-04406124v1
	The Silene latifolia genome and its giant Y chromosome Carol Moraga , Catarina Branco , Quentin Rougemont , Paris Veltsos , Pavel Jedlička 2024 Pré-publication, Document de travail hal-04515245v1
	The Silene latifolia genome and its giant Y chromosome Carol Moraga , Catarina Branco , Quentin Rougemont , Paris Veltsos , Pavel Jedlička 2023 Pré-publication, Document de travail hal-04293712v1
	From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals,PocilloporaandPorites Romane Deshuraud , Alexandre Ottaviani , Julie Poulain , Marine Leprêtre , Odette Beluche 2023 Pré-publication, Document de travail hal-04195332v1
	Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition Caroline Belser , Julie Poulain , Karine Labadie , Frederick Gavory , Adriana Alberti 2022 Pré-publication, Document de travail cea-03713370v2

	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. Poster de conférence 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 Poster de conférence 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 Poster de conférence 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 Poster de conférence 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 Poster de conférence hal-02797182v1

Caroline Menguy

Publications

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

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

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

Diversity of the Pacific Ocean coral reef microbiome

Host transcriptomic plasticity and photosymbiotic fidelity underpin $Pocillopora$ acclimatization across thermal regimes in the Pacific Ocean

Genomic adaptation of the picoeukaryote $Pelagomonas\ calceolata$ to iron-poor oceans revealed by a chromosome-scale genome sequence

Epigenomic and structural events preclude recombination in Brassica napus

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

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

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

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

Chromosome-scale assembly of the yellow mealworm genome

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

Diversity and biogeography of bathyal and abyssal seafloor bacteria and archaea along a Mediterranean-Atlantic gradient

Population genomics of apricots unravels domestication history and adaptive events

Long-read assembly of the Brassica napus reference genome Darmor-bzh

BiSCoT: improving large eukaryotic genome assemblies with optical maps

Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa

Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers

Draft Genome Sequence of Tubulinosema ratisbonensis , a Microsporidian Species Infecting the Model Organism Drosophila melanogaster

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean

A reference genome for pea provides insight into legume genome evolution

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

Oak genome reveals facets of long lifespan

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Genome assembly using Nanopore-guided long and error-free DNA reads

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

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

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

The DNA sequence and analysis of human chromosome 14

TARA Pacific CTAX colony morphological annotations release version 1_1

TARA Pacific Bleaching Prevalence of Sampling Sites (Islands)

Tara Pacific V9 18S rDNA metabarcoding dataset

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

Tara Pacific 16S rRNA data analysis release

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

Tara Pacific ITS2 Symbiodiniaceae data release version 1

European mink (Mustela lutreola) reference genome and population genomics

The Pisum Genus: Getting out of Pea Soup!

The pea genome

Towards the genome sequence of pea : a tribute to Mendel

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

Approches bioinformatiques pour l'exploration des génomes et de la biodiversité

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

The Silene latifolia genome and its giant Y chromosome

The Silene latifolia genome and its giant Y chromosome

From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals,PocilloporaandPorites

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

LONG DNA TECHNOLOGIES EVALUATION FOR PLANT STRUCTURAL VARIATIONS DETECTION : NANOPORE ONT SEQUENCING vs BIONANO GENOMICS OPTICAL MAPPING

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

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

Optical Mapping with the Saphyr System on Plant Genomes

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