Cécile Donnadieu

68
Documents

Présentation

Domaines de recherche

Sciences de l'environnement Sciences du Vivant [q-bio]

Compétences

Project Leader Manager Quality Genomic sequencing

Publications

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Publications

Image document

Pig and quail CpG methylation datasets from short and long read sequencing technologies

Paul Terzian , Céline Vandecasteele , Joanna Lledo , Rémy-Félix Serre , Jules Sabban et al.
Scientific Data , 2025, 12 (1), pp.556. ⟨10.1038/s41597-025-04769-4⟩
Article dans une revue hal-05039144 v1
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Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae

Heiner Kuhl , Peter Euclide , Christophe Klopp , Cédric Cabau , Margot Zahm et al.
BMC Biology, 2024, 22 (1), pp.141. ⟨10.1186/s12915-024-01935-9⟩
Article dans une revue hal-04638789 v1
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Massive detection of cryptic recessive genetic defects in dairy cattle mining millions of life histories

Florian Besnard , Ana Guintard , Cécile Grohs , Laurence Guzylack-Piriou , Margarita Cano et al.
Genome Biology, 2024, 25 (1), pp.248. ⟨10.1186/s13059-024-03384-7⟩
Article dans une revue hal-04714371 v1
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Detection of DNA methylation signatures through the lens of genomic imprinting

Jean-Noël Hubert , Nathalie Iannuccelli , Cédric Cabau , Eva Jacomet , Yvon Billon et al.
Scientific Reports, 2024, 14 (1), pp.1694. ⟨10.1038/s41598-024-52114-3⟩
Article dans une revue hal-04453257 v1
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Suspicions of two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France

Enora Dupas , Karine Durand , Adrien Rieux , Martial Briand , Olivier Pruvost et al.
Communications Biology, 2023, 6 (1), pp.103. ⟨10.1038/s42003-023-04499-6⟩
Article dans une revue hal-03975291 v1
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Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets

Jeanlin Jourdain , Harmonie Barasc , Thomas Faraut , Anne Calgaro , Nathalie Bonnet et al.
Genome Research, 2023, 33 (6), pp.957-971. ⟨10.1101/gr.277787.123⟩
Article dans une revue hal-04170739 v1
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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 et al.
Science, 2023, 379 (6639), pp.1316-1323. ⟨10.1126/science.adc9691⟩
Article dans une revue hal-04065852 v1
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Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols

Florence Nicot , Pauline Trémeaux , Justine Latour , Nicolas Jeanne , Noémie Ranger et al.
Journal of Medical Virology, 2023, 95 (1), pp.e28123. ⟨10.1002/jmv.28123⟩
Article dans une revue hal-03988344 v1
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Size Fractionation of Milliliter DNA Samples in Minutes Controlled by an Electric Field of ∼10 V

Paul Bruand , Inga Tijunelyte , Adrien Castinel , Cécile Donnadieu , Pierre Joseph et al.
Analytical Chemistry, 2023, 95 (49), pp.18099-18106. ⟨10.1021/acs.analchem.3c03187⟩
Article dans une revue hal-04322873 v1
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The genomics of linkage drag in inbred lines of sunflower

Kaichi Huang , Mojtaba Jahani , Jérôme Gouzy , Alexandra Legendre , Sébastien Carrere et al.
Proceedings of the National Academy of Sciences of the United States of America, 2023, 120 (14), pp.e2205783119. ⟨10.1073/pnas.2205783119⟩
Article dans une revue hal-04198273 v1
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A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling

Camille Eché , Carole Iampietro , Clément Birbes , Andreea Dréau , Claire Kuchly et al.
Scientific Data , 2023, 10 (1), pp.369. ⟨10.1038/s41597-023-02249-1⟩
Article dans une revue (data paper) hal-04122201 v1
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Genome structures resolve the early diversification of teleost fishes

Elise Parey , Alexandra Louis , Jérôme Montfort , Olivier Bouchez , Céline Roques et al.
Science, 2023, 379 (6632), pp.572-575. ⟨10.1101/2022.04.07.487469⟩
Article dans une revue hal-03765882 v1

Transcriptional response to host chemical cues underpins the expansion of host range in a fungal plant pathogen lineage

Stefan Kusch , Justine Larrouy , Heba Ibrahim , Shantala Mounichetty , Noémie Gasset et al.
The International Society of Microbiologial Ecology Journal, 2022, 16 (1), pp.138-148. ⟨10.1038/s41396-021-01058-x⟩
Article dans une revue hal-03331958 v1
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Generation of a chromosome‐level genome assembly for Pacific halibut ( Hippoglossus stenolepis ) and characterization of its sex‐determining genomic region

Andrew J. Jasonowicz , Anna Simeon , Margot Zahm , Cédric Cabau , Christophe Klopp et al.
Molecular Ecology Resources, 2022, 22 (7), pp.2685-2700. ⟨10.1111/1755-0998.13641⟩
Article dans une revue hal-03737450 v1
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The genomic history and global expansion of domestic donkeys

Evelyn Todd , Laure Tonasso-Calvière , Loreleï Chauvey , Stéphanie Schiavinato , Antoine Fages et al.
Science, 2022, 377 (6611), pp.1172-1180. ⟨10.1126/science.abo3503⟩
Article dans une revue hal-03827857 v1
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An ancient truncated duplication of the anti‐Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

Ming Wen , Qiaowei Pan , Elodie Jouanno , Jérôme Montfort , Margot Zahm et al.
Molecular Ecology Resources, 2022, 22 (6), pp.2411-2428. ⟨10.1111/1755-0998.13620⟩
Article dans une revue hal-03652234 v1
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Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing

Sébastien Lhomme , Justine Latour , Nicolas Jeanne , Pauline Trémeaux , Noémie Ranger et al.
Viruses, 2021, 13 (12), pp.2544. ⟨10.3390/v13122544⟩
Article dans une revue hal-03771640 v1
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Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2

Chloé Dimeglio , Marine Milhes , Jean-Michel Loubes , Noémie Ranger , Jean-Michel Mansuy et al.
Viruses, 2021, 13 (5), ⟨10.3390/v13050898⟩
Article dans une revue hal-03739146 v1
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Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

Aurélie Allais-Bonnet , Aurélie Hintermann , Marie-Christine Deloche , Raphael Cornette , Philippe Bardou et al.
Molecular Biology and Evolution, 2021, ⟨10.1093/molbev/msab021⟩
Article dans une revue hal-03164832 v1
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Influence of age on the spread of SARS-CoV-2 variant B.1.1.7

Chloé Dimeglio , Florence Nicot , Marcel Miedougé , Jean-Loup Chappert , Cécile Donnadieu et al.
Journal of Clinical Virology, 2021, 141, ⟨10.1016/j.jcv.2021.104872⟩
Article dans une revue hal-03739196 v1
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A supernumerary “B-sex” chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus

Boudjema Imarazene , Kang Du , Séverine Beille , Elodie Jouanno , Romain Feron et al.
Current Biology, 2021, 31 (21), pp.4800-4809.e9. ⟨10.1016/j.cub.2021.08.030⟩
Article dans une revue hal-03337251 v1
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Characterization of a Y‐specific duplication/insertion of the anti‐Mullerian hormone type II receptor gene based on a chromosome‐scale genome assembly of yellow perch, Perca flavescens

Romain Feron , Margot Zahm , Cédric Cabau , Christophe Klopp , Céline Roques et al.
Molecular Ecology Resources, 2020, 20 (2), pp.531-543. ⟨10.1111/1755-0998.13133⟩
Article dans une revue hal-02623895 v1

A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass ( Carex sp.)

Stefan Kusch , Heba Ibrahim , Catherine Zanchetta , Celine Lopez-Roques , Cécile Donnadieu et al.
Molecular Plant-Microbe Interactions, 2020, 33 (7), pp.880-883. ⟨10.1094/MPMI-03-20-0060-A⟩
Article dans une revue hal-02900377 v1

Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing

Lucas Torres , Andreanna Welch , Catherine Zanchetta , R. Terry Chesser , Maxime Manno et al.
Mitochondrial DNA Part A, 2019, 30 (2), pp.256-263. ⟨10.1080/24701394.2018.1484116⟩
Article dans une revue hal-01851856 v1
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Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing.

Guillaume Croville , Guillaume Le Loc'H , Catherine Zanchetta , Maxime Manno , Christelle Camus-Bouclainville et al.
Journal of Virological Methods, 2018, 261, pp.34-39. ⟨10.1016/j.jviromet.2018.08.003⟩
Article dans une revue hal-02626516 v1
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The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

Mathieu Gautier , Junichi Yamaguchi , Julien Foucaud , Anne Loiseau , Aurélien Ausset et al.
Current Biology, 2018, 28 (20), pp.1-7. ⟨10.1016/j.cub.2018.08.023⟩
Article dans une revue hal-01864435 v1
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Population genomics of picophytoplankton unveils novel chromosome hypervariability

Romain Blanc-Mathieu , Marc Krasovec , Maxime Hebrard , Sheree Yau , Elodie Desgranges et al.
Science Advances , 2017, 3 (7), pp.e1700239. ⟨10.1126/sciadv.1700239⟩
Article dans une revue lirmm-01842137 v1
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The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Hélène Badouin , Jerome Gouzy , Christopher Grassa , Florent Murat , S Evan Staton et al.
Nature, 2017, 546 (7656), pp.148-152. ⟨10.1038/nature22380⟩
Article dans une revue hal-01603287 v1
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A panel of embryonic stem cell lines reveals the variety and dynamic of pluripotent states in rabbits

Pierre Osteil , Anaïs Moulin , Claire Santamaria , Thierry Joly , Luc Jouneau et al.
Stem Cell Reports, 2016, 7 (3), pp.383-398. ⟨10.1016/j.stemcr.2016.07.022⟩
Article dans une revue hal-02639328 v1

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

Baptiste Mayjonade , Jerome Gouzy , Cécile Donnadieu , Nicolas Pouilly , William Marande et al.
Biotechniques, 2016, 61 (4), pp.203-205. ⟨10.2144/000114460⟩
Article dans une revue hal-01608743 v1
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Correction : Design and Characterization of a 52K SNP Chip for Goats

Gwenola Tosser-Klopp , Philippe Bardou , Olivier Bouchez , Cédric Cabau , Richard Crooijmans et al.
PLoS ONE, 2016, 11 (3), pp.Non Paginé. ⟨10.1371/journal.pone.0152632⟩
Article dans une revue hal-01602260 v1
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Reinforcement of STAT3 activity reprogrammes human embryonic stem cells to naive-like pluripotency

Hongwei Chen , Irène Aksoy , Fabrice Gonnot , Pierre Osteil , Maxime Aubry et al.
Nature Communications, 2015, 6 (1), ⟨10.1038/ncomms8095⟩
Article dans une revue hal-01997120 v1
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The characterization of novel tissue microbiota using an optimized 16S metagenomic sequencing pipeline

Jérôme J. Lluch , Florence Servant , Sandrine Païssé , Carine Valle , Sophie Valiere et al.
PLoS ONE, 2015, 10 (11), pp.1-22. ⟨10.1371/journal.pone.0142334⟩
Article dans une revue hal-02637487 v1
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Novel Avian Coronavirus and Fulminating Disease in Guinea Fowl, France

Etienne Liais , Guillaume Croville , Jérôme J. Mariette , Maxence Delverdier , Marie-Noêlle Lucas et al.
Emerging Infectious Diseases, 2014, 20 (1), pp.105-108. ⟨10.3201/eid2001.130774⟩
Article dans une revue hal-02638202 v1

Development of SNP-genotyping arrays in two shellfish species

S. Lapegue , E Harrang , S Heurtebise , E Flahauw , C Donnadieu et al.
Molecular Ecology, 2014, 14 (4), pp.820-830. ⟨10.1111/1755-0998.12230⟩
Article dans une revue hal-01082464 v1
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A 3.7 Mb deletion encompassing ZEB2 causes a novel polled and multisystemic syndrome in the progeny of a somatic mosaic bull

Aurelien Capitan , Aurélie Allais-Bonnet , Alain Pinton , Brigitte Marquant-Le Guienne , Daniel Le Bourhis et al.
PLoS ONE, 2012, 7, online (11), Non paginé. ⟨10.1371/journal.pone.0049084⟩
Article dans une revue hal-01019835 v1
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Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea

Chrystel Deulvot , Hélène Charrel , Amandine Marty , Françoise Jacquin , Cecile Donnadieu et al.
BMC Genomics, 2010, 11 (august), Non paginé. ⟨10.1186/1471-2164-11-468⟩
Article dans une revue hal-02665874 v1
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The construction of a cattle pangenome for 14 French dairy and beef breeds provides new insights into their genetic diversity.

Valentin Sorin , Marie-Pierre Sanchez , Carole Iampietro , Camille Eché , Amandine Suin et al.
75th Annual Meeting of the European Federation of Animal Science, EAAP, Sep 2024, Florence, Italy. pp.288
Communication dans un congrès hal-04694228 v1

Genotyping a thousand animals using low coverage sequencing and imputation

Cervin Guyomar , Denis Milan , Christophe Klopp , Cécile Donnadieu , Bertrand Servin et al.
Genotoul biostat bioinfo day, Genotoul, Nov 2023, Toulouse, France
Communication dans un congrès hal-04669286 v1
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Improvement of the Bos taurus Genome Assembly using New Sequencing Technologies

Camille Eché , Carole Iampietro , Clement Birbes , Andreea Dreau , Claire Kuchly et al.
Discoveries Roadshow 2023 - PacBio, PacBio, May 2023, Paris, France
Communication dans un congrès hal-04096124 v1
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The benefits of long read HiFi sequencing for metabarcoding analysis

Adrien Castinel , Jean Mainguy , Sylvie Combes , Carole Iampietro , Christine Gaspin et al.
PACBIO DISCOVERIES ROADSHOW PARIS, PACBIO, May 2022, Paris, France
Communication dans un congrès hal-03740586 v1
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Transgenerational epigenetics in quail

Chloé Cerutti , Sophie Leroux , Paul Terzian , Joanna Lledo , David Gourichon et al.
Genotoul Biostat Bioinfo Day, Dec 2022, Castanet-Tolosan, France
Communication dans un congrès hal-03957296 v1
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The benefits of long read HiFi sequencing for metagenomic analysis

Adrien Castinel , Jean Mainguy , Sylvie Combes , Carole Iampietro , Christine Gaspin et al.
France génomique - VIIème Animation Wetlab et Bioinfo, Nov 2022, Strasbourg, France
Communication dans un congrès hal-03896074 v1

Targeting the pig imprintome

Jean-Noël Hubert , Nathalie Iannuccelli , Cédric Cabau , Rémy-Félix Serre , Céline Vandecasteele et al.
Advances in Genome Biology and Technology Agriculture (AGBT-Ag), Apr 2022, San Diego, United States
Communication dans un congrès hal-04099166 v1

metagWGS : a workflow to analyse short or long HiFi metagenomic reads

Joanna Fourquet , Maïna Vienne , Jean Mainguy , Vincent Darbot , Pierre Martin et al.
Bioinfo Biosta Genotoul day, Dec 2022, Castanet Tolosan, France
Communication dans un congrès hal-03944382 v1

In search of the honey bee centromeres: regions with tandem repeats high at content and low recombination rates

Alain Vignal , Sonia E Eynard , Christophe Klopp , Bertrand Servin , Kamila Canale-Tabet et al.
9th European Congress of Apidology, Sep 2022, Belgrade, Serbia
Communication dans un congrès hal-03855207 v1

De novo genome assembly of a western European Apis mellifera mellifera black bee

Alain Vignal , Sonia E Eynard , Christophe Klopp , Kamila Canale Tabet , William Marande et al.
Apimondia, Sep 2019, MOntréal, Canada
Communication dans un congrès hal-04796454 v1
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Détection moléculaire et caractérisation de virus respiratoires du canard par une approche de séquençage à haut débit

Etienne Liais , Guillaume Croville , Jérôme J. Mariette , Christophe Klopp , Cécile Donnadieu et al.
Journée SEVAB, Nov 2012, Toulouse, France
Communication dans un congrès hal-01191337 v1
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Transgenerational epigenetics in quail: targeting DNA methylation patterns to address the interplay between genetic and epigenetic mechanisms

Stacy Rousse , Chloé Cerutti , Sophie Leroux , Paul Terzian , Joanna Lledo et al.
Ecology and Evolution, Oct 2024, Lyon, France
Poster de conférence hal-04770637 v1
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Targeting the pig imprintome with EM-seq

Jean-Noël Hubert , Nathalie Iannuccelli , Mathilde Perret , Cédric Cabau , Eva Jacomet et al.
2024 Environnemental and Agronomical Genomics Symposium, Feb 2024, Toulouse, France.
Poster de conférence hal-04668372 v1

Whole genome sequencing and epigenotyping for multiple generations of selection using Oxford Nanopore Technology

Sonia E Eynard , Cécile Donnadieu , Loïc Flatres-Grall , Carole Iampietro , Sandrine Lagarrigue et al.
International congress in Ecology and Evolution, Oct 2024, Lyon, France
Poster de conférence hal-04796434 v1
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Whole genome sequencing and epigenotyping for multiple generations of selection using Oxford Nanopore Technology

Sonia E Eynard , Cécile Donnadieu , Loïc Flatres-Grall , Carole Iampietro , Sandrine Lagarrigue et al.
Environmental and Agronomical Genomics Symposium, Feb 2024, Toulouse, France. , pp.118, Book of abstracts
Poster de conférence hal-04473354 v1
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Benchmarking of sequencing technologies for CpG methylation detection: applications to quail and pig

Céline Vandecasteele , Paul Terzian , Joanna Lledo , Rémy-Félix Serre , Jules Sabban et al.
London Calling 2024, May 2024, London, France
Poster de conférence hal-04638952 v1
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Major contribution to the bovine pangenome: whole genome sequences, SNPs, and structural variants of 154 bulls from 14 breeds

Amandine Suin , Camille Marcuzzo , Camille Eché , Andreea Dréau , Clément Birbes et al.
Plant and Genome San Diego 2024, Jan 2024, San Diego, United States
Poster de conférence hal-04432840 v1
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A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling

Camille Eché , Carole Iampietro , Clément Birbes , Andreea Dréau , Claire Kuchly et al.
Plant and Genome San Diego 2024, Jan 2024, San Diego (California), United States. 10, 2024
Poster de conférence hal-04432803 v1
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Search for new mutations in cattle by systemac whole genome resequencing

Mekki Boussaha , Camille Eché , Clémentine Escouflaire , Cécile Grohs , Carole Iampietro et al.
39th International Society of Animal Genetics Conference, Jul 2023, Cape Town / Le Cap, South Africa
Poster de conférence hal-04170956 v1

L’évolution de l’épigénétique au cours de plusieurs générations de sélection

Sonia E Eynard , Cécile Donnadieu , Loïc Flatres-Grall , Carole Iampietro , Sandrine Lagarrigue et al.
EpiPhase, Oct 2023, Jouy en Josas, France
Poster de conférence hal-04796446 v1
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Transgenerational epigenetics in quail: whole genome DNA methylation analysis

Chloé Cerutti , Sophie Leroux , Paul Terzian , Joanna Lledo , David Gourichon et al.
Epigenetic Inheritance: Impact for Biology and Society, Aug 2023, Zurich, Switzerland
Poster de conférence hal-04212971 v1
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metagWGS: a workflow to analyse short and long HiFi metagenomic reads

Joanna Fourquet , Maïna Vienne , Jean Mainguy , Vincent Darbot , Pierre Martin et al.
ECCB2022, Sep 2022, Sitges, Spain
Poster de conférence hal-03788263 v1

Vers une carte de l'imprintome porcin

Jean-Noël Hubert , Nathalie Iannuccelli , Cédric Cabau , Rémy-Félix Serre , Céline Vandecasteele et al.
Journées Scientifiques du Département de Génétique Animale, Sep 2022, Bordeaux, France
Poster de conférence hal-04099355 v1
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Transgenerational epigenetics in quail

Chloé Cerutti , Sophie Leroux , Paul Terzian , Joanna Lledo , David Gourichon et al.
ECCB2022 - 21st European Conference on Computational Biology, Sep 2022, Sitges, Spain
Poster de conférence hal-03935584 v1
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Structural variants detection and de novo genome assembly of a maize line

Carole Iampietro , Camille Eché , Clément Birbes , Arnaud Di Franco , Andreea Dréau et al.
Plant & Animal Genome Conference (PAG) 2022, Jan 2022, San Diego, United States
Poster de conférence hal-03541379 v1
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Implementation of new methods for metagenomics analysis using PacBio HiFi sequencing

Adrien Castinel , Jean Mainguy , Sylvie Combes , Carole Iampietro , Christine Gaspin et al.
Plant & Animal Genome Conference (PAG) 2022, Jan 2022, San Diego, United States
Poster de conférence hal-03541346 v1
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Preliminary results from Nanopore Q20+ sequencing

Claire Kuchly , Jules Sabban , Eden Darnige , Camille Eché , Amandine Suin et al.
JOBIM 2022 : Journées Ouvertes Biologie Informatique Mathématiques, Jul 2022, RENNES, France. 2022
Poster de conférence hal-03719401 v1
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Strengths and limits of long read metabarcoding

Jean Mainguy , Adrien Castinel , Olivier Bouchez , Sylvie Combes , Carole Iampietro et al.
ECCB 2022, Sep 2022, Meliá Sitges, Spain
Poster de conférence hal-03848228 v1
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De novo assembly of 90 bovines genomes using PacBio CLR application comparison and optimization

Camille Marcuzzo , Amandine Suin , Camille Eché , Andreea Dreau , Clément Birbes et al.
Assemblée générale France Génomique, Jun 2022, Paris, France
Poster de conférence hal-04590746 v1
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De novo assembly of bovine genome using PacBio applications

Camille Eché , Clément Birbes , Carole Iampietro , Andreea Dréau , Claire Kuchly et al.
SMRT Leiden 2021 – Young Investigator Virtual Conference, May 2021, virtuel, Netherlands
Poster de conférence hal-03541224 v1
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Improving microbial taxonomic profiling with long read technologies

Jean Mainguy , Adrien Castinel , Olivier Bouchez , Sylvie Combes , Carole Iampietro et al.
JOBIM2020, Jun 2020, Montpellier (virtuel), France
Poster de conférence hal-03177058 v1