Author: "Cécile Donnadieu" - Searchworks@Jio Institute Digital Library Search Results

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1. Massive detection of cryptic recessive genetic defects in dairy cattle mining millions of life histories

Author: Florian Besnard, Ana Guintard, Cécile Grohs, Laurence Guzylack-Piriou, Margarita Cano, Clémentine Escouflaire, Chris Hozé, Hélène Leclerc, Thierry Buronfosse, Lucie Dutheil, Jeanlin Jourdain, Anne Barbat, Sébastien Fritz, Marie-Christine Deloche, Aude Remot, Blandine Gaussères, Adèle Clément, Marion Bouchier, Elise Contat, Anne Relun, Vincent Plassard, Julie Rivière, Christine Péchoux, Marthe Vilotte, Camille Eche, Claire Kuchly, Mathieu Charles, Arnaud Boulling, Guillaume Viard, Stéphanie Minéry, Sarah Barbey, Clément Birbes, Coralie Danchin-Burge, Frédéric Launay, Sophie Mattalia, Aurélie Allais-Bonnet, Bérangère Ravary, Yves Millemann, Raphaël Guatteo, Christophe Klopp, Christine Gaspin, Carole Iampietro, Cécile Donnadieu, Denis Milan, Marie-Anne Arcangioli, Mekki Boussaha, Gilles Foucras, Didier Boichard, and Aurélien Capitan
Subjects: Data science, Recessive genetic defects, Livestock, Large-scale genotyping, Whole-genome sequencing, Inbreeding depression, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract: Abstract Background Dairy cattle breeds are populations of limited effective size, subject to recurrent outbreaks of recessive defects that are commonly studied using positional cloning. However, this strategy, based on the observation of animals with characteristic features, may overlook a number of conditions, such as immune or metabolic genetic disorders, which may be confused with pathologies of environmental etiology. Results We present a data mining framework specifically designed to detect recessive defects in livestock that have been previously missed due to a lack of specific signs, incomplete penetrance, or incomplete linkage disequilibrium. This approach leverages the massive data generated by genomic selection. Its basic principle is to compare the observed and expected numbers of homozygotes for sliding haplotypes in animals with different life histories. Within three cattle breeds, we report 33 new loci responsible for increased risk of juvenile mortality and present a series of validations based on large-scale genotyping, clinical examination, and functional studies for candidate variants affecting the NOA1, RFC5, and ITGB7 genes. In particular, we describe disorders associated with NOA1 and RFC5 mutations for the first time in vertebrates. Conclusions The discovery of these many new defects will help to characterize the genetic basis of inbreeding depression, while their management will improve animal welfare and reduce losses to the industry.
Published: 2024
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2. The black honey bee genome: insights on specific structural elements and a first step towards pangenomes

Author: Sonia E. Eynard, Christophe Klopp, Kamila Canale-Tabet, William Marande, Céline Vandecasteele, Céline Roques, Cécile Donnadieu, Quentin Boone, Bertrand Servin, and Alain Vignal
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses. Results Pacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for re-estimation of the recombination rate, which was over-estimated in some previous studies due to mis-assemblies, which resulted in spurious inversions in the older reference genomes. The sequence continuity obtained was very high and the only limit towards continuous chromosome-wide sequences seemed to be due to tandem repeat arrays that were usually longer than 10 kb and that belonged to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome to genotype two structural variants by a pangenome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76% for the two variants. Conclusions Our new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance by including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pangenomes.
Published: 2024
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3. Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae

Author: Heiner Kuhl, Peter T. Euclide, Christophe Klopp, Cédric Cabau, Margot Zahm, Céline Lopez-Roques, Carole Iampietro, Claire Kuchly, Cécile Donnadieu, Romain Feron, Hugues Parrinello, Charles Poncet, Lydia Jaffrelo, Carole Confolent, Ming Wen, Amaury Herpin, Elodie Jouanno, Anastasia Bestin, Pierrick Haffray, Romain Morvezen, Taina Rocha de Almeida, Thomas Lecocq, Bérénice Schaerlinger, Dominique Chardard, Daniel Żarski, Wesley A. Larson, John H. Postlethwait, Serik Timirkhanov, Werner Kloas, Sven Wuertz, Matthias Stöck, and Yann Guiguen
Subjects: Sex-determination, Genome, Perches, Pikeperches, Sex chromosomes, Biology (General), QH301-705.5
Abstract: Abstract Background The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. Results We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19–27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. Conclusions Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
Published: 2024
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4. Detection of DNA methylation signatures through the lens of genomic imprinting

Author: Jean-Noël Hubert, Nathalie Iannuccelli, Cédric Cabau, Eva Jacomet, Yvon Billon, Rémy-Félix Serre, Céline Vandecasteele, Cécile Donnadieu, and Julie Demars
Subjects: Medicine, Science
Abstract: Abstract Genomic imprinting represents an original model of epigenetic regulation resulting in a parent-of-origin expression. Despite the critical role of imprinted genes in mammalian growth, metabolism and neuronal function, there is no molecular tool specifically targeting them for a systematic evaluation. We show here that enzymatic methyl-seq consistently outperforms the bisulfite-based standard in capturing 165 candidate regions for genomic imprinting in the pig. This highlights the potential for a turnkey, fully customizable and reliable capture tool of genomic regions regulated by cytosine methylation in any population of interest. For the field of genomic imprinting, it opens up the possibility of detecting multilocus imprinting variations across the genome, with implications for basic research, agrigenomics and clinical practice.
Published: 2024
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5. A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling

Author: Camille Eché, Carole Iampietro, Clément Birbes, Andreea Dréau, Claire Kuchly, Arnaud Di Franco, Christophe Klopp, Thomas Faraut, Sarah Djebali, Adrien Castinel, Matthias Zytnicki, Erwan Denis, Mekki Boussaha, Cécile Grohs, Didier Boichard, Christine Gaspin, Denis Milan, and Cécile Donnadieu
Subjects: Science
Abstract: Abstract Inspired by the production of reference data sets in the Genome in a Bottle project, we sequenced one Charolais heifer with different technologies: Illumina paired-end, Oxford Nanopore, Pacific Biosciences (HiFi and CLR), 10X Genomics linked-reads, and Hi-C. In order to generate haplotypic assemblies, we also sequenced both parents with short reads. From these data, we built two haplotyped trio high quality reference genomes and a consensus assembly, using up-to-date software packages. The assemblies obtained using PacBio HiFi reaches a size of 3.2 Gb, which is significantly larger than the 2.7 Gb ARS-UCD1.2 reference. The BUSCO score of the consensus assembly reaches a completeness of 95.8%, among highly conserved mammal genes. We also identified 35,866 structural variants larger than 50 base pairs. This assembly is a contribution to the bovine pangenome for the “Charolais” breed. These datasets will prove to be useful resources enabling the community to gain additional insight on sequencing technologies for applications such as SNP, indel or structural variant calling, and de novo assembly.
Published: 2023
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6. Suspicions of two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France

Author: Enora Dupas, Karine Durand, Adrien Rieux, Martial Briand, Olivier Pruvost, Amandine Cunty, Nicolas Denancé, Cécile Donnadieu, Bruno Legendre, Céline Lopez-Roques, Sophie Cesbron, Virginie Ravigné, and Marie-Agnès Jacques
Subjects: Biology (General), QH301-705.5
Abstract: A genomic investigation into strains of the plant pathogen, Xylella fastidiosa, in France indicate an American origin with two waves of invasion.
Published: 2023
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7. Imputed genomes of historical horses provide insights into modern breeding

Author: Evelyn T. Todd, Aurore Fromentier, Richard Sutcliffe, Yvette Running Horse Collin, Aude Perdereau, Jean-Marc Aury, Camille Èche, Olivier Bouchez, Cécile Donnadieu, Patrick Wincker, Ted Kalbfleisch, Jessica L. Petersen, and Ludovic Orlando
Subjects: Equine genetics, Genomics, Phylogenetics, Science
Abstract: Summary: Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski’s horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with higher genetic similarity to those in the past and unveiled increased inbreeding in recent times. We genotyped variants associated with appearance and behavior to uncover previously unknown characteristics of these important historical horses. Overall, we provide insights into the history of Thoroughbred and Clydesdale breeds and highlight genomic changes in the endangered Przewalski’s horse following a century of captive breeding.
Published: 2023
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8. Rabbit targeted genomic sequences after heterologous hybridization using human exome

Author: Nathalie Iannuccelli, Julien Sarry, Yvon Billon, Patrick Aymard, Virginie Helies, Cédric Cabau, Cécile Donnadieu, and Julie Demars
Subjects: Rabbit, Targeted DNA sequencing, Capture, Exome, Human, Heterologous hybridization, Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract: Abstract Objective Causal mutations for major genes that underlie a broad range of morphological traits are often located within exons of genes that then affect protein functions. Non-model organism genetic studies are not easy to perform due to the lack of genome-wide molecular tools such as SNP genotyping array. Genotyping-By-Sequencing (GBS) methods offer an alternative. Consequently, we used this approach that is focused on the exome to target and identify major genes in rabbit populations. Data description We used a heterologous enrichment method before sequencing, allowing us to capture the rabbit exome using the marketed human panel since mammal protein coding genes are well conserved across the phylogenic tree of species. This targeted strategy was performed on 52 French rabbits from 5 different French strains (Californian, New-Zealand, Castor, Chinchilla and Laghmere). We generated 3.4 billion sequencing reads and approximately 29–140 million of reads per DNA sample. The expected exome coverage per sample ranged between 118 and 566X. The present dataset could be useful for the scientific community working on rabbit species in order to (i) improve the annotation of the rabbit reference genome Oryctolagus cuniculus (OryCun2.0), (ii) enrich the characterization of polymorphisms segregating in rabbits and (iii) evaluate the genetic biodiversity in different rabbit strains. Raw sequences were deposited in the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory- European Bioinformatics Institute (EMBL-EBI) data portal under bioproject accession number PRJEB37917.
Published: 2022
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9. Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity

Author: Yusuke Takehana, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, Olivier Bouchez, Cécile Donnadieu, Celia Barrachina, Laurent Journot, Mari Kawaguchi, Shigeki Yasumasu, Satoshi Ansai, Kiyoshi Naruse, Koji Inoue, Chuya Shinzato, Manfred Schartl, Yann Guiguen, and Amaury Herpin
Subjects: medaka, evolution, whole genome sequencing, long reads, genetic map, transcriptome, adaptation, salinity, Genetics, QH426-470
Abstract: The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behavior, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies. Complementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6,3 Mbp and a L50 of 37 scaffolds. We identified 21454 predicted transcripts for a total transcriptome size of 57, 146, 583 bps. We provide here a high-quality chromosome scale draft genome assembly of the euryhaline Javafish medaka (321 scaffolds anchored on 24 chromosomes (representing 97.7% of the total bases)), and give emphasis on the evolutionary adaptation to salinity.
Published: 2020
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10. Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing

Author: Sébastien Lhomme, Justine Latour, Nicolas Jeanne, Pauline Trémeaux, Noémie Ranger, Marion Migueres, Gérald Salin, Cécile Donnadieu, and Jacques Izopet
Subjects: SARS-CoV-2, PacBio SMRT sequencing, Illumina sequencing, S1 domain, clade, lineage, Microbiology, QR1-502
Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antibodies is the main point of the current monitoring. This study examines the feasibility of predicting the variant lineage and monitoring the appearance of reported mutations by sequencing only the region encoding the S1 domain by Pacific Bioscience Single Molecule Real-Time sequencing (PacBio SMRT). Using the PacBio SMRT system, we successfully sequenced 186 of the 200 samples previously sequenced with the Illumina COVIDSeq (whole genome) system. PacBio SMRT detected mutations in the S1 domain that were missed by the COVIDseq system in 27/186 samples (14.5%), due to amplification failure. These missing positions included mutations that are decisive for lineage assignation, such as G142D (n = 11), N501Y (n = 6), or E484K (n = 2). The lineage of 172/186 (92.5%) samples was accurately determined by analyzing the region encoding the S1 domain with a pipeline that uses key positions in S1. Thus, the PacBio SMRT protocol is appropriate for determining virus lineages and detecting key mutations.
Published: 2021
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11. Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2

Author: Chloé Dimeglio, Marine Milhes, Jean-Michel Loubes, Noémie Ranger, Jean-Michel Mansuy, Pauline Trémeaux, Nicolas Jeanne, Justine Latour, Florence Nicot, Cécile Donnadieu, and Jacques Izopet
Subjects: SARS-CoV-2, public health, statistical model, variant B.1.1.7, Microbiology, QR1-502
Abstract: The spread of SARS-CoV-2 and the resulting disease COVID-19 has killed over 2.6 million people as of 18 March 2021. We have used a modified susceptible, infected, recovered (SIR) epidemiological model to predict how the spread of the virus in regions of France will vary depending on the proportions of variants and on the public health strategies adopted, including anti-COVID-19 vaccination. The proportion of SARS-CoV-2 variant B.1.1.7, which was not detected in early January, increased to become 60% of the forms of SARS-CoV-2 circulating in the Toulouse urban area at the beginning of February 2021, but there was no increase in positive nucleic acid tests. Our prediction model indicates that maintaining public health measures and accelerating vaccination are efficient strategies for the sustained control of SARS-CoV-2.
Published: 2021
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12. A Panel of Embryonic Stem Cell Lines Reveals the Variety and Dynamic of Pluripotent States in Rabbits

Author: Pierre Osteil, Anaïs Moulin, Claire Santamaria, Thierry Joly, Luc Jouneau, Maxime Aubry, Yann Tapponnier, Catherine Archilla, Barbara Schmaltz-Panneau, Jérôme Lecardonnel, Harmonie Barasc, Nathalie Mouney-Bonnet, Clémence Genthon, Alain Roulet, Cécile Donnadieu, Hervé Acloque, Elen Gocza, Véronique Duranthon, Marielle Afanassieff, and Pierre Savatier
Subjects: Medicine (General), R5-920, Biology (General), QH301-705.5
Abstract: Conventional rabbit embryonic stem cell (ESC) lines are derived from the inner cell mass (ICM) of pre-implantation embryos using methods and culture conditions that are established for primate ESCs. In this study, we explored the capacity of the rabbit ICM to give rise to ESC lines using conditions similar to those utilized to generate naive ESCs in mice. On single-cell dissociation and culture in fibroblast growth factor 2 (FGF2)-free, serum-supplemented medium, rabbit ICMs gave rise to ESC lines lacking the DNA-damage checkpoint in the G1 phase like mouse ESCs, and with a pluripotency gene expression profile closer to the rabbit ICM/epiblast profiles. These cell lines can be converted to FGF2-dependent ESCs after culture in conventional conditions. They can also colonize the rabbit pre-implantation embryo. These results indicate that rabbit epiblast cells can be coaxed toward different types of pluripotent stem cells and reveal the dynamics of pluripotent states in rabbit ESCs.
Published: 2016
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13. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

Author: Baptiste Mayjonade, Jérôme Gouzy, Cécile Donnadieu, Nicolas Pouilly, William Marande, Caroline Callot, Nicolas Langlade, and Stéphane Muños
Subjects: DNA extraction, long-read sequencing, PacBio, Biology (General), QH301-705.5
Abstract: De novo sequencing of complex genomes is one of the main challenges for researchers seeking high-quality reference sequences. Many de novo assemblies are based on short reads, producing fragmented genome sequences. Third-generation sequencing, with read lengths >10 kb, will improve the assembly of complex genomes, but these techniques require high-molecular-weight genomic DNA (gDNA), and gDNA extraction protocols used for obtaining smaller fragments for short-read sequencing are not suitable for this purpose. Methods of preparing gDNA for bacterial artificial chromosome (BAC) libraries could be adapted, but these approaches are time-consuming, and commercial kits for these methods are expensive. Here, we present a protocol for rapid, inexpensive extraction of high-molecular-weight gDNA from bacteria, plants, and animals. Our technique was validated using sunflower leaf samples, producing a mean read length of 12.6 kb and a maximum read length of 80 kb.
Published: 2016
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14. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

Author: Baptiste Mayjonade, Jérôme Gouzy, Cécile Donnadieu, Nicolas Pouilly, William Marande, Caroline Callot, Nicolas Langlade, and Stéphane Muños
Subjects: Biology (General), QH301-705.5
Abstract: Protocol Summary Third-generation sequencing, with read lengths >10 kb, will improve the assembly of complex genomes, but these techniques require high-molecular-weight genomic DNA (gDNA), and gDNA extraction protocols used for obtaining smaller fragments for short-read sequencing are not suitable for this purpose. Methods of preparing gDNA for bacterial artificial chromosome (BAC) libraries could be adapted, but these approaches are time-consuming, and commercial kits for these methods are expensive. Here, we present a protocol for rapid, inexpensive extraction of high-molecular-weight gDNA from bacteria, plants, and animals. Our technique was validated using sunflower leaf samples, producing a mean read length of 12.6 kb and a maximum read length of 80 kb.
Published: 2017
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15. Novel Avian Coronavirus and Fulminating Disease in Guinea Fowl, France

Author: Etienne Liais, Guillaume Croville, Jérôme Mariette, Maxence Delverdier, Marie-Noëlle Lucas, Christophe Klopp, Jérôme Lluch, Cécile Donnadieu, James S. Guy, Léni Corrand, Mariette F. Ducatez, and Jean-Luc Guérin
Subjects: coronavirus, guinea fowl, metagenomics, next-generation sequencing, viruses, France, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: For decades, French guinea fowl have been affected by fulminating enteritis of unclear origin. By using metagenomics, we identified a novel avian gammacoronavirus associated with this disease that is distantly related to turkey coronaviruses. Fatal respiratory diseases in humans have recently been caused by coronaviruses of animal origin.
Published: 2014
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16. Correction: Design and Characterization of a 52K SNP Chip for Goats.

Author: Gwenola Tosser-Klopp, Philippe Bardou, Olivier Bouchez, Cédric Cabau, Richard Crooijmans, Yang Dong, Cécile Donnadieu-Tonon, André Eggen, Henri C M Heuven, Saadiah Jamli, Abdullah Johari Jiken, Christophe Klopp, Cynthia T Lawley, John McEwan, Patrice Martin, Carole R Moreno, Philippe Mulsant, Ibouniyamine Nabihoudine, Eric Pailhoux, Isabelle Palhière, Rachel Rupp, Julien Sarry, Brian L Sayre, Aurélie Tircazes, Jun Wang, Wen Wang, Wenguang Zhang, and International Goat Genome Consortium
Subjects: Medicine, Science
Published: 2016
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17. The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.

Author: Jérôme Lluch, Florence Servant, Sandrine Païssé, Carine Valle, Sophie Valière, Claire Kuchly, Gaëlle Vilchez, Cécile Donnadieu, Michael Courtney, Rémy Burcelin, Jacques Amar, Olivier Bouchez, and Benjamin Lelouvier
Subjects: Medicine, Science
Abstract: BackgroundSubstantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin). However, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples.ResultsWe have optimized a specific 16S rDNA-targeted metagenomics sequencing (16S metabarcoding) pipeline based on the Illumina MiSeq technology for the analysis of bacterial DNA in human and animal tissues. This was successfully achieved in various mouse tissues despite the high abundance of eukaryotic DNA and PCR inhibitors in these samples. We extensively tested this pipeline on mock communities, negative controls, positive controls and tissues and demonstrated the presence of novel tissue specific bacterial DNA profiles in a variety of organs (including brain, muscle, adipose tissue, liver and heart).ConclusionThe high throughput and excellent reproducibility of the method ensured exhaustive and precise coverage of the 16S rDNA bacterial variants present in mouse tissues. This optimized 16S metagenomic sequencing pipeline will allow the scientific community to catalogue the bacterial DNA profiles of different tissues and will provide a database to analyse host/bacterial interactions in relation to homeostasis and disease.
Published: 2015
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18. Design and characterization of a 52K SNP chip for goats.

Author: Gwenola Tosser-Klopp, Philippe Bardou, Olivier Bouchez, Cédric Cabau, Richard Crooijmans, Yang Dong, Cécile Donnadieu-Tonon, André Eggen, Henri C M Heuven, Saadiah Jamli, Abdullah Johari Jiken, Christophe Klopp, Cynthia T Lawley, John McEwan, Patrice Martin, Carole R Moreno, Philippe Mulsant, Ibouniyamine Nabihoudine, Eric Pailhoux, Isabelle Palhière, Rachel Rupp, Julien Sarry, Brian L Sayre, Aurélie Tircazes, Jun Wang, Wen Wang, Wenguang Zhang, and International Goat Genome Consortium
Subjects: Medicine, Science
Abstract: The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.
Published: 2014
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19. A 3.7 Mb deletion encompassing ZEB2 causes a novel polled and multisystemic syndrome in the progeny of a somatic mosaic bull.

Author: Aurélien Capitan, Aurélie Allais-Bonnet, Alain Pinton, Brigitte Marquant-Le Guienne, Daniel Le Bourhis, Cécile Grohs, Stéphan Bouet, Laëtitia Clément, Laura Salas-Cortes, Eric Venot, Stéphane Chaffaux, Bernard Weiss, Arnaud Delpeuch, Guy Noé, Marie-Noëlle Rossignol, Sarah Barbey, Dominique Dozias, Emilie Cobo, Harmonie Barasc, Aurélie Auguste, Maëlle Pannetier, Marie-Christine Deloche, Emeline Lhuilier, Olivier Bouchez, Diane Esquerré, Gérald Salin, Christophe Klopp, Cécile Donnadieu, Céline Chantry-Darmon, Hélène Hayes, Yves Gallard, Claire Ponsart, Didier Boichard, and Eric Pailhoux
Subjects: Medicine, Science
Abstract: Polled and Multisystemic Syndrome (PMS) is a novel developmental disorder occurring in the progeny of a single bull. Its clinical spectrum includes polledness (complete agenesis of horns), facial dysmorphism, growth delay, chronic diarrhea, premature ovarian failure, and variable neurological and cardiac anomalies. PMS is also characterized by a deviation of the sex-ratio, suggesting male lethality during pregnancy. Using Mendelian error mapping and whole-genome sequencing, we identified a 3.7 Mb deletion on the paternal bovine chromosome 2 encompassing ARHGAP15, GTDC1 and ZEB2 genes. We then produced control and affected 90-day old fetuses to characterize this syndrome by histological and expression analyses. Compared to wild type individuals, affected animals showed a decreased expression of the three deleted genes. Based on a comparison with human Mowat-Wilson syndrome, we suggest that deletion of ZEB2, is responsible for most of the effects of the mutation. Finally sperm-FISH, embryo genotyping and analysis of reproduction records confirmed somatic mosaicism in the founder bull and male-specific lethality during the first third of gestation. In conclusion, we identified a novel locus involved in bovid horn ontogenesis and suggest that epithelial-to-mesenchymal transition plays a critical role in horn bud differentiation. We also provide new insights into the pathogenicity of ZEB2 loss of heterozygosity in bovine and humans and describe the first case of male-specific lethality associated with an autosomal locus in a non-murine mammalian species. This result sets PMS as a unique model to study sex-specific gene expression/regulation.
Published: 2012
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20. 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

Author: Ming Wen, Qiaowei Pan, Elodie Jouanno, Jerome Montfort, Margot Zahm, Cédric Cabau, Christophe Klopp, Carole Iampietro, Céline Roques, Olivier Bouchez, Adrien Castinel, Cécile Donnadieu, Hugues Parrinello, Charles Poncet, Elodie Belmonte, Véronique Gautier, Jean-Christophe Avarre, Remi Dugue, Rudhy Gustiano, Trần Thị Thúy Hà, Marc Campet, Kednapat Sriphairoj, Josiane Ribolli, Fernanda L. de Almeida, Thomas Desvignes, John H. Postlethwait, Christabel Floi Bucao, Marc Robinson-Rechavi, Julien Bobe, Amaury Herpin, Yann Guiguen, Hunan Normal University (HNU), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Lausanne = University of Lausanne (UNIL), Plateforme Bio-Informatique - Génotoul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-BioInfOmics, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Research Institute of Freshwater Fisheries (CRIFI-RIFF), Research Institute for Aquaculture, Neovia Asia, Kasetsart University (KU), Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC), Embrapa Amazônia Ocidental, Partenaires INRAE, University of Oregon [Eugene], Swiss Institute of Bioinformatics [Lausanne] (SIB), Swiss Institute of Bioinformatics [Genève] (SIB), National Institutes of Health : R01 OD011116, National Institutes of Health: R35 GM139635, ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-16-CE12-0035,GenoFish,Evolution des génes et des génomes après duplication compléte(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), MING WEN, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, QIAOWEI PAN, INRAE, LPGP, ELODIE JOUANNO, INRAE, LPGP, JEROME MONTFORT, INRAE, LPGP, MARGOT ZAHM, Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, CÉDRIC CABAU, SIGENAE, GenPhySE, Université de Toulouse, INRAE, CHRISTOPHE KLOPP, SIGENAE, CAROLE IAMPIETRO, INRAE, CÉLINE ROQUES, INRAE, OLIVIER BOUCHEZ, INRAE, ADRIEN CASTINEL, INRAE, CÉCILE DONNADIEU, INRAE, HUGUES PARRINELLO, Montpellier GenomiX, CHARLES PONCET, GDEC Gentyane, INRAE, Université Clermont Auvergne, ELODIE BELMONTE, GDEC Gentyane, INRAE, Université Clermont Auvergne, VÉRONIQUE GAUTIER, GDEC Gentyane, INRAE, Université Clermont Auvergne, JEAN-CHRISTOPHE AVARRE, ISEM, CNRS, IRD, Univ Montpellier, REMI DUGUE, ISEM, CNRS, IRD, Univ Montpellier, RUDHY GUSTIANO, Research Institute of Freshwater Fisheries (CRIFI-RIFF), TRÂN THI THÚY HÀ, Research Institute for Aquaculture, MARC CAMPET, Neovia Asia, KEDNAPAT SRIPHAIROJ, Faculty of Natural Resources and Agro-Industry, JOSIANE RIBOLLI, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Universidade Federal de Santa Catarina, FERNANDA LOUREIRO ALMEIDA OSULLIVAN, CPAA, THOMAS DESVIGNES, Institute of Neuroscience, University of Oregon, JOHN H. POSTLETHWAIT, Institute of Neuroscience, University of Oregon, CHRISTABEL FLOI BUCAO, Department of Ecology and Evolution, University of Lausanne, MARC ROBINSON-RECHAVI, Department of Ecology and Evolution, University of Lausanne, JULIEN BOBE, INRAE, LPGP, AMAURY HERPIN, INRAE, LPGP, and YANN GUIGUEN, INRAE, LPGP.
Subjects: Male, Male genome assembly, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Receptors, Peptide, Animals, Catfishes/genetics, Phylogeny, Receptors, Peptide/genetics, Receptors, Transforming Growth Factor beta/genetics, Y Chromosome/genetics, amhr2, evolution, male genome assembly, pangasiid catfishes, sex determination, Evolution, Pangasiid catfishes, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Sex determination, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Peixe-gato, Y Chromosome, Genetics, Hormônio, Receptors, Transforming Growth Factor beta, Catfishes, Ecology, Evolution, Behavior and Systematics, Biotechnology
Abstract: The evolution of sex determination (SD) mechanisms in teleost fishes is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified, even sometimes among closely related species. Pangasiids are a group of economically important catfishes in many South-Asian countries, but little is known about their sex determination system. Here, we generated novel genomic resources for 12 Pangasiid species and provided a first characterization of their SD system. Based on an Oxford Nanopore long-read chromosome-scale high quality genome assembly of the striped catfish Pangasianodon hypophthalmus, we identified a duplication of the anti-Müllerian hormone receptor type II gene (amhr2), which was further characterized as being sex-linked in males and expressed only in testicular samples. These first results point to a male-specific duplication on the Y chromosome (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Short-read genome sequencing and reference-guided assembly of 11 additional Pangasiid species, along with sex-linkage studies, revealed that this truncated amhr2by duplication is also conserved as a male-specific gene in many Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication / insertion event at the root of the Siluroidei radiation that is dated around 100 million years ago. Altogether these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiid catfishes, a finding that highlights the recurrent usage of the transforming growth factor β pathway in teleost sex determination and brings another empirical case towards the understanding of the dynamics or stability of sex determination systems.
Published: 2022
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21. Generation of a chromosome‐level genome assembly for Pacific halibut ( Hippoglossus stenolepis ) and characterization of its sex‐determining genomic region

Author: Andrew J. Jasonowicz, Anna Simeon, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, Carole Iampietro, Jérôme Lluch, Cécile Donnadieu, Hugues Parrinello, Daniel P. Drinan, Lorenz Hauser, Yann Guiguen, and Josep V. Planas
Subjects: Male, Fishes, Genetics, Animals, Female, Flounder, Genomics, Chromosomes, Ecosystem, Ecology, Evolution, Behavior and Systematics, Genome-Wide Association Study, Biotechnology
Abstract: The Pacific halibut (Hippoglossus stenolepis) is a key species in the North Pacific Ocean and Bering Sea ecosystems, where it also supports important fisheries. However, the lack of genomic resources limits our understanding of evolutionary, environmental and anthropogenic forces affecting key life history characteristics of Pacific halibut and prevents the application of genomic tools in fisheries management and conservation efforts. In the present study, we report on the first generation of a high-quality chromosome-level assembly of the Pacific halibut genome, with an estimated size of 602 Mb, 24 chromosome-length scaffolds that contain 99.8% of the assembly and a N
Published: 2022
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22. A methyl-seq tool to capture genomic imprinted loci

Author: Jean-Noël, Hubert, primary, Nathalie, Iannuccelli, additional, Cédric, Cabau, additional, Eva, Jacomet, additional, Yvon, Billon, additional, Rémy-Felix, Serre, additional, Céline, Vandecasteele, additional, Cécile, Donnadieu, additional, and Julie, Demars, additional
Published: 2023
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23. The genomics of linkage drag in inbred lines of sunflower

Author: Kaichi Huang, Mojtaba Jahani, Jérôme Gouzy, Alexandra Legendre, Sébastien Carrere, José Miguel Lázaro-Guevara, Eric Gerardo González Segovia, Marco Todesco, Baptiste Mayjonade, Nathalie Rodde, Stéphane Cauet, Isabelle Dufau, S. Evan Staton, Nicolas Pouilly, Marie-Claude Boniface, Camille Tapy, Brigitte Mangin, Alexandra Duhnen, Véronique Gautier, Charles Poncet, Cécile Donnadieu, Tali Mandel, Sariel Hübner, John M. Burke, Sonia Vautrin, Arnaud Bellec, Gregory L. Owens, Nicolas Langlade, Stéphane Muños, and Loren H. Rieseberg
Subjects: Multidisciplinary
Abstract: Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here, we analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge-regression best linear unbiased prediction (BLUP) model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including >3,000 new genes. While introgressions reduced genetic load at protein-coding sequences, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low-frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.
Published: 2023
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24. Genome structures resolve the early diversification of teleost fishes

Author: Elise Parey, Alexandra Louis, Jerome Montfort, Olivier Bouchez, Céline Roques, Carole Iampietro, Jerome Lluch, Adrien Castinel, Cécile Donnadieu, Thomas Desvignes, Christabel Floi Bucao, Elodie Jouanno, Ming Wen, Sahar Mejri, Ron Dirks, Hans Jansen, Christiaan Henkel, Wei-Jen Chen, Margot Zahm, Cédric Cabau, Christophe Klopp, Andrew W. Thompson, Marc Robinson-Rechavi, Ingo Braasch, Guillaume Lecointre, Julien Bobe, John H. Postlethwait, Camille Berthelot, Hugues Roest Crollius, Yann Guiguen, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Oregon [Eugene], Université de Lausanne = University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Hunan Normal University (HNU), Florida Atlantic University [Boca Raton], Future Genomics Technologies, Universiteit Leiden, Norwegian University of Life Sciences (NMBU), National Taiwan University [Taiwan] (NTU), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Western Michigan University [Kalamazoo], Michigan State University [East Lansing], Michigan State University System, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Génomique fonctionnelle comparative - Comparative functional genomics, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This work was supported by the Agence Nationale de la Recherche, France (ANR) on the GenoFish project, 2016–2021 (grant No. ANR-16-CE12-003) to H.R.C., C.B., J.B., J.H.P., M.R.C., and Y.G., and by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by ANR (grant No. ANR-10-INBS-09) to C.D. Part of the fellowship to E.P. was supported by funds from the European Union Horizon 2020 research and innovation program under Grant Agreement No 817923 (AQUA-FAANG). M.R.-R. was supported by the Swiss National Science Foundation grant 31003A_173048. J.H.P and I.B were supported by the National Institutes of Health under grant agreement No. R01OD011116. W.J.C. was supported by MOST grants No. 111-2611-M-002-025, 110-2611-M-002-013, and 108-2611-M-002-012-MY2., ANR-16-CE12-0035,GenoFish,Evolution des génes et des génomes après duplication compléte(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 817923,H2020,H2020-EU.3.2.1.1., H2020-EU.3.2.3.1.,AQUA-FAANG(2019), DYnamique et Organisation des GENomes - Equipe de l'IBENS (DYOGEN), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Institute of Oceanography [Taipei], Plateforme Bio-Informatique - Génotoul, Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-BioInfOmics, Génétique des génomes - Genetics of Genomes (UMR 3525), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Swiss National Science Foundation grant 31003A_173048, National Institute of Health under grant agreement No R01OD011116, and Muséum national d'Histoire naturelle (MNHN)
Subjects: Animals, Zebrafish/genetics, Fishes/genetics, Eels/genetics, Biological Evolution, Phylogeny, Genome, Evolution, Molecular, Multidisciplinary, [SDV]Life Sciences [q-bio], [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, [SDV.BID]Life Sciences [q-bio]/Biodiversity
Abstract: Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (bony-tongues) in a monophyletic group sister to all other teleosts, i.e., the Clupeocephala lineage. This finding resolves over 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.One-Sentence SummaryWhole-genome analyses place Elopomorpha (tarpons, eels) and Osteoglossomorpha (bony-tongues) as sister groups at the deepest branching of crown teleosts.
Published: 2023
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25. Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols

Author: Florence Nicot, Pauline Trémeaux, Justine Latour, Nicolas Jeanne, Noémie Ranger, Stéphanie Raymond, Chloé Dimeglio, Gérald Salin, Cécile Donnadieu, and Jacques Izopet
Subjects: Infectious Diseases, Virology
Abstract: Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Single-molecule real-time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole-genome sequencing (WGS) of SARS-CoV-2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher (p 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3-99.5]) than with the amplicon protocol (99.3% [IQR: 69.9-99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for C
Published: 2022
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26. The genomic history and global expansion of domestic donkeys

Author: Evelyn T. Todd, Laure Tonasso-Calvière, Loreleï Chauvey, Stéphanie Schiavinato, Antoine Fages, Andaine Seguin-Orlando, Pierre Clavel, Naveed Khan, Lucía Pérez Pardal, Laura Patterson Rosa, Pablo Librado, Harald Ringbauer, Marta Verdugo, John Southon, Jean-Marc Aury, Aude Perdereau, Emmanuelle Vila, Matilde Marzullo, Ornella Prato, Umberto Tecchiati, Giovanna Bagnasco Gianni, Antonio Tagliacozzo, Vincenzo Tinè, Francesca Alhaique, João Luís Cardoso, Maria João Valente, Miguel Telles Antunes, Laurent Frantz, Beth Shapiro, Daniel G. Bradley, Nicolas Boulbes, Armelle Gardeisen, Liora Kolska Horwitz, Aliye Öztan, Benjamin S. Arbuckle, Vedat Onar, Benoît Clavel, Sébastien Lepetz, Ali Akbar Vahdati, Hossein Davoudi, Azadeh Mohaseb, Marjan Mashkour, Olivier Bouchez, Cécile Donnadieu, Patrick Wincker, Samantha A. Brooks, Albano Beja-Pereira, Dong-Dong Wu, and Ludovic Orlando
Subjects: Ancestry, Multidisciplinary, Asia, Genome, DNA, Equidae, Genomics, Insights, Gene flow, Domestication, Africa, Animals, Humans, Equids, Phylogeny
Abstract: Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa similar to 5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant similar to 200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military. French National Research Agency (ANR) ANR-10-INBS-09 info:eu-repo/semantics/publishedVersion
Published: 2022

27. The genomics of linkage drag in sunflower

Author: Kaichi Huang, Mojtaba Jahani, Jérôme Gouzy, Alexandra Legendre, Sebastien Carrere, José Miguel Lázaro-Guevara, Eric Gerardo González Segovia, Marco Todesco, Baptiste Mayjonade, Nathalie Rodde, Stéphane Cauet, Isabelle Dufau, S Evan Staton, Nicolas Pouilly, Marie-Claude Boniface, Camille Tapy, Brigitte Mangin, Alexandra Duhnen, Véronique Gautier, Charles Poncet, Cécile Donnadieu, Tali Mandel, Sariel Hübner, John M. Burke, Sonia Vautrin, Arnaud Bellec, Gregory L. Owens, Nicolas Langlade, Stéphane Muños, and Loren H. Rieseberg
Abstract: Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here we comprehensively analyzed the genomic and phenotypic impacts of wild introgressions into cultivated sunflower to estimate the impacts of linkage drag. First, we generated new reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge regression model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including > 3,000 new genes. While introgressions reduced genetic load at protein-coding sequences and positively affected traits associated with abiotic stress resistance, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, pre-breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.
Published: 2022
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28. A tunable filter for high molecular weight DNA selection and linked-read sequencing

Author: Adrien Castinel, Frederic Ginot, Aurélien Bancaud, Audrey Gibert, Olivier Bouchez, Géraud Bouwmans, Juan-Luis Fuentes Rojas, Cécile Donnadieu, Audrey Boutonnet, Laurent Bigot, Nicolas Milon, Karen Baudelle, Équipe Micro-Nanofluidique pour les sciences de la vie et de l’environnement (LAAS-MILE), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Picometrics Technologies, ANR-16-CE18-0028,MicroLAS,µ-Laboratoire d'Analyse et de Séparation des chromosomes : développement d'un outil pour le typage rapide des bactéries, levures et cellules de mammifères(2016), ANR-16-ASTR-0020,BIOPULSE,Dispositif de détection biologique ultrasensible de pathogènes prélevés par air pulsé.(2016), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J), Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Photonique (Photonique), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Computer science, Sequencing data, Biomedical Engineering, Bioengineering, 02 engineering and technology, Third generation sequencing, Computational biology, Biochemistry, [SPI.MAT]Engineering Sciences [physics]/Materials, 03 medical and health sciences, Cucumis melo, Particle Size, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], Throughput (business), ComputingMilieux_MISCELLANEOUS, Selection (genetic algorithm), 030304 developmental biology, 0303 health sciences, DNA, Sequence Analysis, DNA, General Chemistry, 021001 nanoscience & nanotechnology, Molecular Weight, genomic DNA, Filter (video), [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, 0210 nano-technology, Block size, High molecular weight dna
Abstract: International audience; In third generation sequencing, the production of quality data requires the selection of molecules longer than ∼20 kbp, but the size selection threshold of most purification technologies is smaller than this target. Here, we describe a technology operated in a capillary with a tunable selection threshold in the range of 3 to 40 kbp controlled by an electric field. We demonstrate that the selection cut-off is sharp, the purification yield is high, and the purification throughput is scalable. We also provide an analytical model that the actuation settings of the filter. The selection of high molecular weight genomic DNA from the melon Cucumis melo L., a diploid organism of ∼0.45 Gbp, is then reported. Linked-read sequencing data show that the N50 phase block size, which scores the correct representation of two chromosomes, is enhanced by a factor of 2 after size selection, establishing the relevance and versatility of our technology.
Published: 2020
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29. Suspicions of two bridgehead invasions ofXylella fastidiosasubsp.multiplexin France

Author: Enora Dupas, Karine Durand, Adrien Rieux, Martial Briand, Olivier Pruvost, Amandine Cunty, Nicolas Denancé, Cécile Donnadieu, Bruno Legendre, Céline Lopez-Roques, Sophie Cesbron, Virginie Ravigné, and Marie-Agnès Jacques
Abstract: Of American origin, a wide diversity ofXylella fastidiosastrains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspeciesmultiplex(ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 × 10-7substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Côte d’Azur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations.
Published: 2022
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30. A supernumerary 'B-sex' chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus

Author: Séverine Beille, Sylvie Rétaux, John H. Postlethwait, Claire Kuchly, Hugues Parrinello, Amaury Herpin, Tomáš Pavlica, Ahmed Al-Rikabi, Christophe Klopp, Cécile Donnadieu, Jorge Torres-Paz, Manfred Schartl, Lisa Gil, Thomas Liehr, Joerg Bohlen, Adrien Castinel, Romain Feron, Yann Guiguen, Céline Lopez-Roques, Margot Zahm, Cédric Cabau, Boudjema Imarazene, Frédéric Veyrunes, Thomas D. Mueller, Elodie Jouanno, Alexandr Sember, Kang Du, Sergey A. Simanovsky, Qiaowei Pan, Julie Perez, Laurent Journot, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Texas State University, Université de Lausanne = University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institute of Animal Physiology and Genetics of the Czech Academy of Sciences (IAPG / CAS), Czech Academy of Sciences [Prague] (CAS), Charles University [Prague] (CU), Jena University Hospital [Jena], A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of Würzburg = Universität Würzburg, University of Oregon [Eugene], This project was supported by funds from the 'Agence Nationale de la Recherche' (ANR/DFG, PhyloSex project, 2014-2016) to Y.G. and M.S. S.R. was supported by grants from an Equipe FRM (Fondation pour la Recherche Médicale, DEQ20150331745) and MITI CNRS (Mission pour les Initiatives Transverses et Interdisciplinaires). J.H.P. was supported by an NIH grant (R35 GM139635). Sequencing was supported by France Génomique as part of an 'Investissement d’avenir' program managed by ANR (contract ANR-10-INBS-09) and by the GET-PACBIO program (Programme opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020). The CytoEvol platform at ISEM was supported by the Labex CeMEB. J.B., T.P., and A.S. were supported by RVO: 67985904 of IAPG CAS, Liběchov. T.P. was supported by the projects of the Czech Ministry of Education (SVV 260571/2021). S.A.S. was supported by the Russian Foundation for Basic Research (RFBR) (18-34-00638). B.I.’s PhD fellowship was supported by the Doctoral School of Ecology, Geosciences, Agronomy, Nutrition of the University of Rennes 1 and INRAE. We are grateful to the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12) for providing help, computing, and storage resources. Funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), University of Lausanne (UNIL), Université de Lausanne (UNIL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Guiguen, Yann, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, and Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID
Subjects: Male, [SDV]Life Sciences [q-bio], Male sex determination, sex determination, Cavefish, B chromosome, Biology, Genome, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Animals, gonads, Gene, genome, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Sexual differentiation, Characidae, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], sex chromosomes, Chromosome, Sex reversal, Biological Evolution, [SDV] Life Sciences [q-bio], Caves, cavefish, gdf6, sex differentiation, Female, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract: Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now.(1,2) B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species(3,4) that have often been considered as selfish genetic elements that behave as genome parasites.(5,6) The observation that in some species Bs can be either restricted or predominant in one sex(7–14) raised the interesting hypothesis that Bs could play a role in sex determination.(15) The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachón cave, we show that Bs are strongly male predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachón cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b (gdf6b). Supporting its role as an MSD gene, we found that the Pachón cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachón cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachón cavefish B is a “B-sex” chromosome that contains duplicated copies of the gdf6b gene, which can promote male sex determination in this species.
Published: 2021
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31. Detection and Typing of a Fowl Adenovirus Type 1 Agent of Pancreatitis in Guinea Fowl

Author: Vincent Blondel, Guillaume Croville, Cécile Donnadieu, Céline Lopez-Roques, Léni Corrand, Maxime Manno, Guillaume Le Loc’h, Jean-Luc Guérin, Marie-Noëlle Lucas, and Maxence Delverdier
Subjects: General Immunology and Microbiology, Phylogenetic tree, Adenoviridae Infections, Aviadenovirus, Outbreak, Biology, medicine.disease, Virology, Genome, Adenoviridae, Fowl adenovirus A, Pancreatitis, Food Animals, medicine, Animals, Animal Science and Zoology, Flock, Nanopore sequencing, Typing, Chickens, Gene, Phylogeny, Poultry Diseases
Abstract: Adenoviral pancreatitis has been amply described for decades in guinea fowl. Although its pathologic picture has been characterized fairly well, its etiology still remains only partially clarified. Based on several outbreaks diagnosed on commercial guinea flocks raised in France since 2017, we performed direct whole-genome sequencing from pancreatic lesional tissue by using the Oxford Nanopore Technologies (ONT) sequencing method. We generated 4781 viral reads and assembled a whole genome of 43,509 bp, clustering within fowl adenovirus type 1 (FAdV-1). A phylogenetic analysis based on a partial sequence of the hexon and short fiber genes on viruses collected in France showed 98.7% and 99.8% nucleotide identity, respectively. Altogether, these results confirm that an FAdV-1 closely related to chicken and other avian strains is the agent of pancreatitis in guinea fowl. This study illustrates the potential of ONT sequencing method to achieve rapid whole-genome sequencing directly from pathologic material.Detección y tipificación de un adenovirus aviar tipo 1 (FAdV-1), agente de pancreatitis en gallinas de Guinea. La pancreatitis adenoviral se ha descrito ampliamente durante décadas en gallinas de Guinea. Aunque su cuadro patológico se ha caracterizado bastante bien, su etiología todavía permanece sólo parcialmente aclarada. Sobre la base de varios brotes diagnosticados en parvadas comerciales de guineas criadas en Francia desde el año 2017, se realizó una secuenciación directa del genoma completo a partir del tejido de la lesión pancreática mediante el método de secuenciación desarrollado por Oxford Nanopore Technologies. Se generaron 4781 lecturas virales y se ensambló un genoma completo de 43,509 pb, que se agrupó dentro del adenovirus aviar tipo 1 (FAdV-1). Un análisis filogenético basado en una secuencia parcial de los genes hexón y de fibra corta de virus recolectados en Francia mostró identidades de nucleótidos de 98.7% y 99.8%, respectivamente. En conjunto, estos resultados confirman que un adenovirus aviar tipo 1 estrechamente relacionado con el pollo y otras cepas aviares es el agente de la pancreatitis en la gallina de Guinea. Este estudio ilustra el potencial de las tecnologías desarrolladas por Oxford Nanopore Thechnologies para lograr una secuenciación rápida de todo el genoma directamente a partir de material patológico.
Published: 2021
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32. Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2

Author: Jean-Michel Loubes, Nicolas Jeanne, Chloé Dimeglio, Florence Nicot, Cécile Donnadieu, Justine Latour, Jean-Michel Mansuy, Pauline Trémeaux, Marine Milhes, Noémie Ranger, Jacques Izopet, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Virologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), KALK, MURIELLE, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 2019-20 coronavirus outbreak, medicine.medical_specialty, COVID-19 Vaccines, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], Disease, 030204 cardiovascular system & hematology, Microbiology, Virus, Article, 03 medical and health sciences, 0302 clinical medicine, SARS-CoV-2, public health, statistical model, variant B.1.1.7, Virology, Epidemiology, medicine, Humans, 030212 general & internal medicine, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Public health, business.industry, Vaccination, COVID-19, QR1-502, [SDV] Life Sciences [q-bio], Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Variant B117, France, Statistical model, business, Epidemiologic Methods
Abstract: International audience; The spread of SARS-CoV-2 and the resulting disease COVID-19 has killed over 2.6 million people as of 18 March 2021. We have used a modified susceptible, infected, recovered (SIR) epidemiological model to predict how the spread of the virus in regions of France will vary depending on the proportions of variants and on the public health strategies adopted, including anti-COVID-19 vaccination. The proportion of SARS-CoV-2 variant B.1.1.7, which was not detected in early January, increased to become 60% of the forms of SARS-CoV-2 circulating in the Toulouse urban area at the beginning of February 2021, but there was no increase in positive nucleic acid tests. Our prediction model indicates that maintaining public health measures and accelerating vaccination are efficient strategies for the sustained control of SARS-CoV-2.
Published: 2021
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33. Influence of age on the spread of SARS-CoV-2 variant B.1.1.7

Author: Jacques Izopet, Chloé Dimeglio, Cécile Donnadieu, Jean-Loup Chappert, Marcel Miedougé, and Florence Nicot
Subjects: 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), business.industry, SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), public health, COVID-19, Virology, Article, Infectious Diseases, age, Mutation, Medicine, Humans, business, variant B.1.1.7
Published: 2021

34. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

Author: Daniele Bigi, Fiona Menzi, Slim Ben Jemaa, Marie-Christine Deloche, Aurélien Capitan, Johannes A. Lenstra, Marina Naval-Sanchez, Ivica Medugorac, Nathalie Hirter, Gwenola Tosser-Klopp, Diane Esquerre, Coralie M. Reich, Julia M. Paris, Rose-Marie Arbogast, Amandine Blin, Abdelhak Boukadiri, Aurélie Hintermann, Julie Rivière, Denis Duboule, Raphaël Cornette, Cécile Donnadieu, Marie-Dominique Wandhammer, Gjoko Bunevski, Louisa Gidney, Michael Stache, Isabelle Palhiere, Renate Schafberg, James Kijas, Claude Guintard, Joséphine Lesur, Jozsef Zakany, Rachel Rupp, Noelle E. Cockett, John Hedges, Ashleigh Haruda, Philippe Bardou, Olivier Putelat, Tracy Hadfield, Alain Pinton, Ockert Greyvenstein, Aurélie Allais-Bonnet, Este Van Marle-Koster, Eric Pailhoux, Coralie Danchin-Burge, David G. Riley, Cécile Grohs, Benjamin J. Hayes, Cord Drögemüller, Allice, Biologie de la Reproduction, Environnement, Epigénétique & Développement (BREED), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École nationale vétérinaire d'Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Martin-Luther-University Halle-Wittenberg, Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Geneva [Switzerland], University of Bologna, Ludwig Maximilian University [Munich] (LMU), Archéologie d'Alsace, Archéologie et histoire ancienne : Méditerranée - Europe (ARCHIMEDE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Texas A&M University [College Station], Utah State University (USU), Université de Carthage - University of Carthage, Ss. Cyril and Methodius University in Skopje, University of Bern, Manx Text, Manx Loaghtan Sheep Breeders (MLSBG), Utrecht University [Utrecht], Rent a Peasant, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Musée Zoologique de Strasbourg, Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Acquisition et Analyse de Données pour l'Histoire naturelle (2AD), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de l'élevage (IDELE), Agriculture Victoria (AgriBio), Tshwane University of Technology [Pretoria] (TUT), Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], CSIRO Agriculture and Food (CSIRO), Ecole Polytechnique Fédérale de Lausanne (EPFL), Collège de France (CdF (institution)), Allais-Bonnet, Aurélie, Hintermann, Aurélie, Deloche, Marie-Christine, Cornette, Raphaël, Bardou, Philippe, Naval-Sanchez, Marina, Pinton, Alain, Haruda, Ashleigh, Grohs, Cécile, Zakany, Jozsef, Bigi, Daniele, Medugorac, Ivica, Putelat, Olivier, Greyvenstein, Ockert, Hadfield, Tracy, Jemaa, Slim Ben, Bunevski, Gjoko, Menzi, Fiona, Hirter, Nathalie, Paris, Julia M, Hedges, John, Palhiere, Isabelle, Rupp, Rachel, Lenstra, Johannes A, Gidney, Louisa, Lesur, Joséphine, Schafberg, Renate, Stache, Michael, Wandhammer, Marie-Dominique, Arbogast, Rose-Marie, Guintard, Claude, Blin, Amandine, Boukadiri, Abdelhak, Rivière, Julie, Esquerré, Diane, Donnadieu, Cécile, Danchin-Burge, Coralie, Reich, Coralie M, Riley, David G, Marle-Koster, Este van, Cockett, Noelle, Hayes, Benjamin J, Drögemüller, Cord, Kijas, Jame, Pailhoux, Eric, Tosser-Klopp, Gwenola, Duboule, Deni, Capitan, Aurélien, École nationale vétérinaire d'Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), École nationale vétérinaire - Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Université de Genève = University of Geneva (UNIGE), University of Bologna/Università di Bologna, Ss. Cyril and Methodius University in Skopje (UKIM), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), and Collège de France - Chaire internationale Évolution des génomes et développement
Subjects: 0106 biological sciences, Male, co-option, translocation, AcademicSubjects/SCI01180, regulatory mutation, 01 natural sciences, Hox genes, Hox gene, genes, 610 Medicine & health, Bilateria, time, Horns, 0303 health sciences, biology, Ecology, 630 Agriculture, Goats, [SDV.BDD.EO] Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Gene Expression Regulation, Developmental, alignment, Morphogenetic field, Biological Evolution, [SDV.BDD.MOR] Life Sciences [q-bio]/Development Biology/Morphogenesis, 590 Animals (Zoology), Haploinsufficiency, transcription, Biometry, Evolution, growth, Locus (genetics), Mice, Transgenic, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, 010603 evolutionary biology, 03 medical and health sciences, goat and sheep genomics, Behavior and Systematics, framework, Genetics, Animals, Allele, Gene, Molecular Biology, Discoveries, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Homeodomain Proteins, locus, Sheep, Horn (anatomy), AcademicSubjects/SCI01130, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, sequence, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Evolutionary biology, Mutation, genome-wide association, 570 Life sciences, goat and sheep genomic
Abstract: In the course of evolution, pecorans (i.e., higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as “headgear,” which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.
Published: 2021
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35. A Supernumerary 'B-Sex' Chromosome Drives Male Sex Determination in the Pachón Cavefish, Astyanax mexicanus

Author: Claire Kuchly, Adrien Castinel, Séverine Beille, Romain Feron, Yann Guiguen, Kang Du, Jorge Torres-Paz, Sylvie Rétaux, Alexandr Sember, Boudjema Imarazene, Margot Zham, Sergey A. Simanovsky, Cédric Cabau, Tomáš Pavlica, Joerg Bohlen, Qiaowei Pan, Cécile Donnadieu, Céline Lopez-Roques, John H. Postlethwait, Manfred Schartl, Elodie Jouanno, Julie Perez, Thomas Liehr, Frédéric Veyrunes, Hugues Parrinello, Lisa Gil, Ahmed Al-Rikabi, Christophe Klopp, Laurent Journot, Amaury Herpin, and Thomas D. Mueller
Subjects: Genetics, B chromosome, GDF6, Male sex determination, Cavefish, Chromosome, Sex reversal, Biology, Gene, Genome
Abstract: Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now. B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species, that have often been considered as selfish genetic elements that behave as genome parasites. The observation that in some species Bs can be either restricted or predominant in one sex raised the interesting hypothesis that Bs could play a role in sex determination. The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachon cave, we show that Bs are strongly male-predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachon cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b gdf6b). Supporting its role as an MSD gene, we found that the Pachon cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachon cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachon cavefish B is a “B-sex” chromosome containing duplicated copies of the gdf6b gene acting as an MSD gene promoting male sex determination in this species.
Published: 2021
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36. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 to Determine the Number and Topology of Horns in Bovidae

Author: Louisa Gidney, Nathalie Hirter, Aurélie Allais-Bonnet, Tracy Hadfield, Coralie M. Reich, Olivier Putelat, Ashleigh Haruda, Marina Naval-Sanchez, Rachel Rupp, Ben J. Hayes, Noelle E. Cockett, Renate Schafberg, van Marle-Koster E, Cord Drögemüller, Philippe Bardou, Marie-Dominique Wandhammer, Cécile Grohs, Coralie Danchin-Burge, Denis Duboule, Fiona Menzi, Amandine Blin, Raphaël Cornette, Isabelle Palhiere, Abdelhak Boukadiri, Marie-Christine Deloche, Johannes A. Lenstra, Rose-Marie Arbogast, Daniele Bigi, Ben Jemaa S, Eric Pailhoux, Stache M, Julia M. Paris, J. Zakany, Aurélie Hintermann, Julie Rivière, Cécile Donnadieu, Aurélien Capitan, Diane Esquerre, Joséphine Lesur, Ivica Medugorac, Alain Pinton, Ockert Greyvenstein, Gjoko Bunevski, Hedges J, David G. Riley, James Kijas, Gwenola Tosser-Klopp, and Claude Guintard
Subjects: biology, Evolutionary biology, Mutant, Locus (genetics), Bovidae, Morphogenetic field, Allele, biology.organism_classification, Haploinsufficiency, Gene, Bilateria
Abstract: In the course of evolution, pecorans (i.e. higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as ‘headgear’, which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats, are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.
Published: 2020
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37. Transcriptional response to host chemical cues underpins expansion of host range in a fungal plant pathogen lineage

Author: Sylvain Raffaele, Catherine Zanchetta, Olivier Navaud, Cécile Donnadieu, Justine Larrouy, Céline Lopez-Roques, Stefan Kusch, Heba M.M. Ibrahim, Malick Mbengue, and Noémie Gasset
Subjects: Transcriptome, biology, Host (biology), Evolutionary biology, Lineage (evolution), Sclerotinia sclerotiorum, Camalexin, Brassicaceae, biology.organism_classification, Genome, Sclerotinia
Abstract: The host range of parasites is an important factor in assessing the dynamics of disease epidemics. The evolution of pathogens to accommodate new hosts may lead to host range expansion, a process the molecular bases of which are largely enigmatic. The fungus Sclerotinia sclerotiorum parasitizes more than 400 plant species from diverse eudicot families while its close relative, S. trifoliorum, is restricted to plants from the Fabaceae family. We analyzed S. sclerotiorum global transcriptome reprogramming on hosts from six botanical families and reveal a flexible, host-specific transcriptional program driven by core and host-response co-expression (SPREx) gene clusters. We generated a chromosome-level genome assembly for S. trifoliorum and found near-complete gene space conservation in broad and narrow host range Sclerotinia species. However, S. trifoliorum showed increased sensitivity to the Brassicaceae defense compound camalexin. Inter-specific transcriptome analyses revealed a lack of transcriptional response to camalexin in S. trifoliorum and provide evidence that cis-regulatory variation associates with the genetic accommodation of Brassicaceae in the Sclerotinia host range. Our work demonstrates adaptive plasticity of a broad host range pathogen with specific responses to different host plants and demonstrates the co-existence of signatures for generalist and polyspecialist life styles in the genome of a plant pathogen. We reason that this mechanism enables the emergence of new disease with no or limited gene flow between strains and species, and could underlie the emergence of new epidemics originating from wild plants in agricultural settings.
Published: 2020
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38. A chromosome-scale genome assembly resource for Myriosclerotinia sulcatula infecting sedge grass (Carex sp.)

Author: Sylvain Raffaele, Heba M.M. Ibrahim, Cécile Donnadieu, Céline Lopez-Roques, Catherine Zanchetta, Stefan Kusch, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Cairo University, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 336808,EC:FP7:ERC,ERC-2013-StG,VARIWHIM(2013), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: long, Physiology, [SDV]Life Sciences [q-bio], Sequence assembly, Fungal pathogen, Genome, 03 medical and health sciences, 0302 clinical medicine, proteomics, Sclerotiniaceae, fungal pathogen, genome, Sclerotinia, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Carex, biology, long read sequencing, Myriosclerotinia sulcatula, Sclerotinia sclerotiorum, read sequencing, General Medicine, 15. Life on land, biology.organism_classification, host specific, Myriosclerotinia, grass plants, Agronomy and Crop Science, 030217 neurology & neurosurgery, Reference genome
Abstract: The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family. file: :Users/u0129515/Sync/My_list_publication/2020/Kusch et al., 2020b.pdf:pdf ispartof: Molecular Plant-Microbe Interactions vol:33 issue:7 pages:880-883 ispartof: location:United States status: Published online
Published: 2020
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39. Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing

Author: Cécile Donnadieu, Guillaume Le Loc’h, Christelle Camus-Bouclainville, Jean-Luc Guérin, Christophe Klopp, Marie-Noëlle Lucas, Mattias Delpont, Guillaume Croville, Catherine Zanchetta, Maxime Manno, Maxence Delverdier, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: 0301 basic medicine, Fowlpox, Time Factors, Genotyping Techniques, 030106 microbiology, Poxviridae Infections, Computational biology, Genome, DNA sequencing, Avipoxvirus, Nanopores, 03 medical and health sciences, Virology, medicine, Animals, Poultry Diseases, Whole genome sequencing, Molecular Epidemiology, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Whole Genome Sequencing, biology, Oxford nanopore MinION, [SDV.BA]Life Sciences [q-bio]/Animal biology, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, Whole-genome surveillance, Fowlpox virus, 3. Good health, 030104 developmental biology, Poxvirus, Minion, Epidemiological Monitoring, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Next-generation sequencing, Nanopore sequencing, Chickens
Abstract: International audience; Avian pox is an infectious disease caused by avipoxviruses (APV), resulting in cutaneous and/or tracheal lesions. Poxviruses share large genome sizes (from 130 to 360 kb), featuring repetitions, deletions or insertions as a result of a long-term recombination history. The increasing performances of next-generation sequencing (NGS) opened new opportunities for surveillance of poxviruses, based on timely and affordable workflows. We investigated the application of the 3rd generation Oxford Nanopore Minion technology to achieve real-time whole-genome sequencing directly from lesions, without any enrichment or isolation step. Fowlpox lesions were sampled on hens, total DNA was extracted and processed for sequencing on a MinION, Oxford Nanopore. We readily generated whole APV genomes from cutaneous or tracheal lesions, without any isolation or PCR-based enrichment: Fowlpox virus reads loads ranged from 0.75% to 2.62% and reads up to 61 kbp were generated and readily assembled into 3 APV complete genomes. This long read size eases the assembly step and lowers the bioinformatics capacity requirements and processing time compared to huge sets of short reads. The complete genome analysis confirmed that these Fowlpox viruses cluster within clade A1 and host full length reticuloendotheliovirus (REV) inserts. The pathobiological relevance of REV insert, although a classical feature of fowlpoxviruses (FPVs), should be further investigated. Surveillance of emerging poxviruses could greatly benefit from real-time whole genome sequencing.
Published: 2018
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40. Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity

Author: Amaury Herpin, Manfred Schartl, Shigeki Yasumasu, Cédric Cabau, Koji Inoue, Margot Zahm, Kiyoshi Naruse, Céline Roques, Célia Barrachina, Cécile Donnadieu, Yusuke Takehana, Christophe Klopp, Yann Guiguen, Mari Kawaguchi, Chuya Shinzato, Olivier Bouchez, Laurent Journot, Satoshi Ansai, Nagahama Institute of Bio-Science and Technology, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sophia University, Laboratory of Bioresources, National Institute for Basic Biology [Okazaki], Atmosphere and Ocean Research Institute [Kashiwa-shi] (AORI), The University of Tokyo (UTokyo), Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg (JMU), Comprehensive Cancer Center Mainfranken, University Hospital, Hagler Institute for Advanced Study and Department of Biology, Texas A&M University System, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hunan Normal University (HNU), This work was supported by a 'Projet Incitatif PHASE department 2015' grant (Grant ID ACI_PHASE, Institut National de la Recherche Agronomique) to AH, a NIBB Collaborative Research Initiative to KN, NIBB individual Collaboration Research Project to MK, and Grants-in-Aid for Young Scientists to YT (Grant ID 16K18590) and MK (Grant ID 16K18593). The GeT and MGX core facilities were supported by France Génomique National infrastructure, funded as partof 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). The GeT core facility was also supported by the 409 GET-PACBIO program (« Programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 »), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-16-COFA-0004,AquaCrispr,Optimization of the CRISPR/Cas9 knock-in technology and application in salmon and trout(2016), ProdInra, Migration, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Optimization of the CRISPR/Cas9 knock-in technology and application in salmon and trout - - AquaCrispr2016 - ANR-16-COFA-0004 - COFA - VALID, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique, Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), The University of Tokyo, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hunan Normal University, This work was supported by a 'Projet Incitatif PHASE department 2015' grant (Grant ID ACI_PHASE, INRAE) to AH, a NIBB Collaborative Research Initiative to KN, NIBB individual Collaboration Research Project to MK, and Grants-in-Aid for Young Scientists to YT (Grant ID 16K18590) and MK (Grant ID 16K18593). AH was additionally funded by the project AquaCRISPR (ANR-16-COFA-0004-01). The GeT and MGX core facilities were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). The GeT core facility was also supported by the GET-PACBIO program (« Programme opérationnel FEDER-FSE Midi-Pyrénées et Garonne 2014-2020 »), ANR-10- INBS0009,INBS,France-Génomique, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), This work was supported by a 'Projet Incitatif PHASE department 2015' grant (Grant ID ACI_PHASE, INRAE) to AH, a NIBB Collaborative Research Initiative to KN, NIBB individual Collaboration Research Project to MK, and Grants-in-Aid for Young Scientists to YT (Grant ID 16K18590) and MK (Grant ID 16K18593). AH was additionally funded by the project AquaCRISPR (ANR-16-COFA-0004-01). The GeT and MGX core facilities were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). The GeT core facility was also supported by the GET-PACBIO program (« Programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 »), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1), and Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE)
Subjects: 0106 biological sciences, Salinity, carte génétique, Evolution, [SDV]Life Sciences [q-bio], séquençage du génome complet, Sequence assembly, [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, QH426-470, Long reads, [INFO] Computer Science [cs], 010603 evolutionary biology, 01 natural sciences, Genome, identification de gènes, adaptation comportementale, 03 medical and health sciences, Genetic map, Genome editing, poisson, Genetics, [INFO]Computer Science [cs], 14. Life underwater, adrianichthyidae, Adaptation, 030304 developmental biology, Whole genome sequencing, tolérance à la salinité, 0303 health sciences, whole genome sequencing, Whole genome sequencing WGS, [SDV.GEN]Life Sciences [q-bio]/Genetics, Phylogenetic tree, biology, Euryhaline, biology.organism_classification, Medaka, osmorégulation, [SDV] Life Sciences [q-bio], [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, espèce modèle, séquençage du génome, eau de mer, Evolutionary biology, Oryzias javanicus, Transcriptome
Abstract: BackgroundThe genus Oryzias is constituted of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behaviour, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies.FindingsComplementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6.3 Mbp and a L50 of 37 scaffolds. We identified 21454 expressed transcripts for a total transcriptome size of 57, 146, 583 bps.ConclusionsWe provide here a high-quality draft genome assembly of the euryhaline Javafish medaka, and give emphasis on the evolutionary adaptation to salinity.
Published: 2019
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41. Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing

Author: Vincent Bretagnolle, Lucas Torres, R. Terry Chesser, Catherine Zanchetta, Cécile Donnadieu, Andreanna J. Welch, Eric Pante, Maxime Manno, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Department of Biosciences [Durham, UK], Durham University, Centre INRA de Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA), Smithsonian Institution, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)
Subjects: 0106 biological sciences, 0301 basic medicine, Mitochondrial DNA, DNA Copy Number Variations, Puffinus, cytochrome-b, Heteroplasmy, DNA, Mitochondrial, Polymorphism, Single Nucleotide, 010603 evolutionary biology, 01 natural sciences, Shearwater, Avian Proteins, Birds, 03 medical and health sciences, RNA, Transfer, Phylogenetics, Gene Duplication, Genetics, Animals, long-range PCR, Molecular Biology, biology, Cytochrome b, Cytochromes b, control region, biology.organism_classification, cytb, tandem repeats, 030104 developmental biology, Procellariiformes, Evolutionary biology, Minion, [SDE]Environmental Sciences
Abstract: International audience; Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon’s shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6, three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.
Published: 2018
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42. The genomic basis of colour pattern polymorphism in the harlequin ladybird

Author: Benjamin Prud'homme, Aurelien Ausset, Arnaud Estoup, Hélène Bergès, Cécile Donnadieu, Julien Foucaud, Junichi Yamaguchi, Heiko Vogel, Danny Severac, Jacques Lagnel, Céline Lopez-Roques, Lian-Sheng Zang, B Gschloessl, Etienne Loire, Anne Loiseau, Benoit Facon, Lori Lawson-Handley, Maxime Manno, Karim Gharbi, Mathieu Gautier, Hugues Parrinello, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de Ressources Génomiques Végétales (CNRGV), Edinburgh Genomics, University of Edinburgh, Norwich Research Park, Evolutionary and Environmental Genomics Group, School of Environmental Sciences, University of Hull, Jilin Agricultural University (JAU), Department of Entomology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ProdInra, Migration, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)
Subjects: 0106 biological sciences, 0303 health sciences, biology, Locus (genetics), biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Phenotype, Harmonia axyridis, Population genomics, 03 medical and health sciences, Taxon, Evolutionary biology, Coccinellidae, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Allele, Gene, 030304 developmental biology
Abstract: Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechanisms generating and maintaining such phenotypic variation within species is essential to comprehending morphological diversity. A common and conspicuous example of discrete phenotypic variation in natural populations of insects is the occurrence of different colour patterns, which has motivated a rich body of ecological and genetic research1–6. The occurrence of dark, i.e. melanic, forms, displaying discrete colour patterns, is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and orange patches on adult elytra varies wildly within species, forming strikingly different complex colour patterns7,8. In the harlequin ladybirdHarmonia axyridis, more than 200 distinct colour forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus9,10. Here, we combined whole-genome sequencing, population genomics, gene expression and functional analyses, to establish that the genepanniercontrols melanic pattern polymorphism inH. axyridis. We show thatpannier, which encodes an evolutionary conserved transcription factor, is necessary for the formation of melanic elements on the elytra. Allelic variation inpannierleads to protein expression in distinct domains on the elytra, and thus determines the distinct colour patterns inH. axyridis. Recombination betweenpannieralleles may be reduced by a highly divergent sequence of ca. 170 kb in thecis-regulatory regions ofpannierwith a 50 kb inversion between colour forms. This likely helps maintaining the distinct alleles found in natural populations. Thus we propose that highly variable discrete colour forms can arise in natural populations throughcis-regulatory allelic variation of a single gene.
Published: 2018
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43. A panel of embryonic stem cell lines reveals the variety and dynamic of pluripotent states in rabbits

Author: Maxime Aubry, Catherine Archilla, Hervé Acloque, Alain Roulet, Cécile Donnadieu, Yann Tapponnier, Thierry Joly, Pierre Osteil, Pierre Savatier, Luc Jouneau, Anaïs Moulin, Véronique Duranthon, Harmonie Barasc, Barbara Schmaltz-Panneau, Jérôme Lecardonnel, Nathalie Mouney-Bonnet, Marielle Afanassieff, Clémence Genthon, Elen Gócza, Claire Santamaria, ProdInra, Migration, Institut cellule souche et cerveau (U846 Inserm - UCBL1), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM), Children's Medical Research Institute [Westmead, Australia], Institut supérieur d'agriculture et d'agroalimentaire Rhône-Alpes (I.S.A.R.A.), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Agricultural Biotechnology Institute, ANR projects PLURABBIT no. PCS-09- GENM-08 and ORYCTOGENE no. ANR-12-RPIB-0013, European Cooperation in Science and Technology (COST) Action (Rabbit Genome Biology [RGB]-Net no. TD1101), HyPharm, Région Rhône-Alpes (ADR CIBLE 2010 project no. R10065CC to Y.T.), Infrastructure Nationale en Biologie et Santé INGESTEM (ANR- 11-INBS-0009), Infrastructure Nationale en Biologie et Santé CRB-Anim (ANR-11-INBS-0003), IHU-B CESAME (ANR-10-IHUB- 003), LabEx DEVweCAN (ANR-10-LABX-0061), LabEx CORTEX (ANR-11-LABX-0042) of the University of Lyon within the program Investissements d’Avenir (ANR-11-IDEX-0007), Fondation pour la Recherche Médicale (FRM SPE20140129375), Institut supérieur d'agriculture et d'agroalimentaire Rhône-Alpes (ISARA), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0301 basic medicine, Cell Culture Techniques, derivation, Embryoid body, Fibroblast growth factor, Biochemistry, Leukemia Inhibitory Factor, generation, Inner cell mass, Cell Self Renewal, Induced pluripotent stem cell, lcsh:QH301-705.5, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Cells, Cultured, reproductive and urinary physiology, Genetics, lcsh:R5-920, Cell Cycle, Biologie du développement, Gene Expression Regulation, Developmental, Embryo, Cell Differentiation, Development Biology, Cell biology, embryonic structures, Rabbits, biological phenomena, cell phenomena, and immunity, lcsh:Medicine (General), Signal Transduction, cellule souche embryonnaire, rabbit, ESC, Biology, Article, Cell Line, 03 medical and health sciences, [SDV.BDD] Life Sciences [q-bio]/Development Biology, pluripotence, Animals, lapin, Embryonic Stem Cells, Janus Kinases, urogenital system, Gene Expression Profiling, Computational Biology, Cell Biology, Embryonic stem cell, MicroRNAs, 030104 developmental biology, Blastocyst, lcsh:Biology (General), Epiblast, Cell culture, Transcriptome, Biomarkers, Developmental Biology
Abstract: Summary Conventional rabbit embryonic stem cell (ESC) lines are derived from the inner cell mass (ICM) of pre-implantation embryos using methods and culture conditions that are established for primate ESCs. In this study, we explored the capacity of the rabbit ICM to give rise to ESC lines using conditions similar to those utilized to generate naive ESCs in mice. On single-cell dissociation and culture in fibroblast growth factor 2 (FGF2)-free, serum-supplemented medium, rabbit ICMs gave rise to ESC lines lacking the DNA-damage checkpoint in the G1 phase like mouse ESCs, and with a pluripotency gene expression profile closer to the rabbit ICM/epiblast profiles. These cell lines can be converted to FGF2-dependent ESCs after culture in conventional conditions. They can also colonize the rabbit pre-implantation embryo. These results indicate that rabbit epiblast cells can be coaxed toward different types of pluripotent stem cells and reveal the dynamics of pluripotent states in rabbit ESCs., Highlights • Generation of rabbit ESCs lacking DNA-damage checkpoint in G1 • Transcriptional profiles of rabbit ESC lines vary depending on culture conditions • Rabbit ESCs can switch between states, revealing plasticity • Some rabbit ESCs can colonize the rabbit pre-implantation embryo, Savatier, Afanassieff, and colleagues report the generation of rabbit ESC lines with gene expression profiles and cell-cycle characteristics closer to those of the rabbit epiblast and mouse ESCs than what was previously reported for rbESC conventional cells. These ESC lines can switch between different states, revealing the dynamics of pluripotency states. Some of these ESC lines acquired the capacity to colonize the rabbit embryo.
Published: 2016
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44. The characterization of novel tissue microbiota using an optimized 16S metagenomic sequencing pipeline

Author: Cécile Donnadieu, Rémy Burcelin, Carine Valle, Claire Kuchly, Jacques Amar, Michael Courtney, Sandrine Païssé, Florence Servant, Jérôme Lluch, Gaelle Vilchez, Benjamin Lelouvier, Sophie Valière, Olivier Bouchez, Département de Génétique Animale [Toulouse], Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Vaiomer, Hôpital de Rangueil, and CHU Toulouse [Toulouse]
Subjects: Sequence analysis, Science, [SDV]Life Sciences [q-bio], mechanism, Eukaryotic DNA replication, Computational biology, Biology, dna, DNA sequencing, law.invention, Microbiology, real time pcr, Mice, 03 medical and health sciences, platform, law, blood, RNA, Ribosomal, 16S, Animals, Humans, [INFO]Computer Science [cs], Microbiome, Polymerase chain reaction, 030304 developmental biology, 0303 health sciences, Multidisciplinary, 030306 microbiology, Microbiota, human body, Animal Structures, Computational Biology, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, biology.organism_classification, DNA extraction, inhibition, Mice, Inbred C57BL, gut, identification, erythrocyte, Metagenomics, Medicine, Bacteria, Research Article
Abstract: BackgroundSubstantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin). However, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples.ResultsWe have optimized a specific 16S rDNA-targeted metagenomics sequencing (16S metabarcoding) pipeline based on the Illumina MiSeq technology for the analysis of bacterial DNA in human and animal tissues. This was successfully achieved in various mouse tissues despite the high abundance of eukaryotic DNA and PCR inhibitors in these samples. We extensively tested this pipeline on mock communities, negative controls, positive controls and tissues and demonstrated the presence of novel tissue specific bacterial DNA profiles in a variety of organs (including brain, muscle, adipose tissue, liver and heart).ConclusionThe high throughput and excellent reproducibility of the method ensured exhaustive and precise coverage of the 16S rDNA bacterial variants present in mouse tissues. This optimized 16S metagenomic sequencing pipeline will allow the scientific community to catalogue the bacterial DNA profiles of different tissues and will provide a database to analyse host/bacterial interactions in relation to homeostasis and disease.
Published: 2015
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45. Reinforcement of STAT3 activity reprogrammes human embryonic stem cells to naive-like pluripotency

Author: Hongwei, Chen, Irène, Aksoy, Fabrice, Gonnot, Pierre, Osteil, Maxime, Aubry, Claire, Hamela, Cloé, Rognard, Arnaud, Hochard, Sophie, Voisin, Emeline, Fontaine, Magali, Mure, Marielle, Afanassieff, Elouan, Cleroux, Sylvain, Guibert, Jiaxuan, Chen, Céline, Vallot, Hervé, Acloque, Clémence, Genthon, Cécile, Donnadieu, John, De Vos, Damien, Sanlaville, Jean-François, Guérin, Michael, Weber, Lawrence W, Stanton, Claire, Rougeulle, Bertrand, Pain, Pierre-Yves, Bourillot, Pierre, Savatier, Institut cellule souche et cerveau / Stem Cell and Brain Research Institute (SBRI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lyon, Biotechnologie et signalisation cellulaire (BSC), Université de Strasbourg (UNISTRA)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS)-Centre National de la Recherche Scientifique (CNRS), Centre épigénétique et destin cellulaire (EDC (UMR_7216)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Laboratoire de Cytogénétique Constitutionnelle [Hospices civils de Lyon], Hospices Civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut cellule souche et cerveau (U846 Inserm - UCBL1), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)
Subjects: Pluripotent Stem Cells, STAT3 Transcription Factor, [SDV]Life Sciences [q-bio], Protein Array Analysis, Feeder Cells, Fibroblasts, Leukemia Inhibitory Factor, Article, Mice, Tamoxifen, Gene Expression Regulation, Animals, Humans, Fibroblast Growth Factor 2, Embryonic Stem Cells, Signal Transduction
Abstract: Leukemia inhibitory factor (LIF)/STAT3 signalling is a hallmark of naive pluripotency in rodent pluripotent stem cells (PSCs), whereas fibroblast growth factor (FGF)-2 and activin/nodal signalling is required to sustain self-renewal of human PSCs in a condition referred to as the primed state. It is unknown why LIF/STAT3 signalling alone fails to sustain pluripotency in human PSCs. Here we show that the forced expression of the hormone-dependent STAT3-ER (ER, ligand-binding domain of the human oestrogen receptor) in combination with 2i/LIF and tamoxifen allows human PSCs to escape from the primed state and enter a state characterized by the activation of STAT3 target genes and long-term self-renewal in FGF2- and feeder-free conditions. These cells acquire growth properties, a gene expression profile and an epigenetic landscape closer to those described in mouse naive PSCs. Together, these results show that temporarily increasing STAT3 activity is sufficient to reprogramme human PSCs to naive-like pluripotent cells., LIF/STAT3 signalling characterizes naive pluripotency in mouse embryonic stem cells (ESCs), but whether this pathway can sustain a similar state in human cells is not completely understood. Here the authors show that LIF stimulation and enhancement of STAT3 activity allow human ESCs to escape from FGF2 dependency and facilitates their entry into a naive-like state of pluripotency.
Published: 2015
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46. Development of SNP genotyping arrays in two shellfish species

Author: Sylvie Lapegue, Philippe Gayral, Estelle Harrang, R. Mahla, Marion Ballenghien, Pierrick Haffray, Cécile Donnadieu, Christophe Klopp, Serge Heurtebise, Emilie Flahauw, L. Barbotte, Lucie Genestout, Laboratoire de Génétique et Pathologie (LGP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génétique et évolution des populations végétales (GEPV), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies, Laboratoire d'hydrodynamique (LadHyX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Institut National de la Recherche Agronomique (INRA), Station SCRIBE, INRA, Syndicat des Sélectionneurs Avicoles Aquacoles Français, Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), GigADN - FranceAgrimer [SIVAL NL: 2010-1021], GAMETOGENES - Agence Nationale de la Recherche 'Genomique animale' Programme [ANR-08-GENM-041], SEAFARE (Sustainable and Environmentally Friendly Aquaculture for the Atlantic Region of Europe) [2009-1/123], Atlantic Area Transnational Program, Hi-Flo, Agence Nationale de la Recherche [ANR-08-blanc-0334-01], European Research Council [ERC PopPhyl 232971], ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008), ANR-08-BLAN-0334,Hi-Flo,The genetic basis and history of adaptive differentiation in high gene flow marine species(2008), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique et Pathologie des Mollusques Marins (LGPMM), Santé, Génétique et Microbiologie des Mollusques (SGMM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: Oyster, Golden Gate technology, Genotyping Techniques, Ostrea edulis, Aquaculture, GoldenGate technology, Polymorphism, Single Nucleotide, biology.animal, Ostrea, Genetics, SNP, Animals, 14. Life underwater, Crassostrea, Genotyping, Ecology, Evolution, Behavior and Systematics, biology, business.industry, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Computational Biology, food and beverages, Pacific oyster, biology.organism_classification, SNP genotyping, Biotechnology, Minor allele frequency, Crassostrea gigas, oysters, business, SNP array
Abstract: International audience; Use of SNPs has been favoured due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two Illumina GoldenGate arrays and genotyped on more than 1000 samples for each species. In each case, oyster samples were obtained from wild and selected populations and from three-generation families seg-regating for traits of interest in aquaculture. The rate of successfully genotyped polymorphic SNPs was about 60% for each species. Effects of SNP origin and quality on genotyping success (Illumina functionality Score) were analy-sed and compared with other model and nonmodel species. Furthermore, a simulation was made based on a subset of the C. gigas SNP array with a minor allele frequency of 0.3 and typical crosses used in shellfish hatcheries. This simulation indicated that at least 150 markers were needed to perform an accurate parental assignment. Such panels might provide valuable tools to improve our understanding of the connectivity between wild (and selected) popula-tions and could contribute to future selective breeding programmes.
Published: 2014
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47. Novel Avian Coronavirus and Fulminating Disease in Guinea Fowl, France

Author: Jérôme Mariette, Guillaume Croville, Mariette F. Ducatez, Marie Noëlle Lucas, Leni Corrand, Jérôme Lluch, Christophe Klopp, Cécile Donnadieu, Jean-Luc Guérin, Maxence Delverdier, Etienne Liais, James S. Guy, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire de Toulouse (ENVT), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), French Ministry of Agriculture, Region Midi-Pyrenees, and French Comite Interprofessionnel de la Pintade
Subjects: Epidemiology, viruses, coronavirus, lcsh:Medicine, Disease, medicine.disease_cause, 0403 veterinary science, Genotype, Avian coronavirus, Galliformes, Phylogeny, Coronavirus, Bird Diseases, Animal biology, 0303 health sciences, Gammacoronavirus, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Microbiology and Parasitology, Dispatch, 04 agricultural and veterinary sciences, Microbiologie et Parasitologie, 3. Good health, Santé publique et épidémiologie, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Spike Glycoprotein, Coronavirus, Coronavirus Infections, france, zoonose, Microbiology (medical), avian coronavirus, animal structures, 040301 veterinary sciences, Molecular Sequence Data, Genome, Viral, virus, lcsh:Infectious and parasitic diseases, Enteritis, 03 medical and health sciences, Biologie animale, medicine, Animals, lcsh:RC109-216, 030304 developmental biology, Essays, métagénomique, metagenomics, Guinea fowl, fulminating disease, lcsh:R, guinea fowl, next-generation sequencing, zoonoses, medicine.disease, biology.organism_classification, Virology, Molecular Typing, séquençage nouvelle génération, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: International audience; For decades, French guinea fowl have been affected by fulminating enteritis of unclear origin. By using metagenomics, we identified a novel avian gammacoronavirus associated with this disease that is distantly related to turkey coronaviruses. Fatal respiratory diseases in humans have recently been caused by coronaviruses of animal origin.
Published: 2014
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48. A 3.7 Mb deletion encompassing ZEB2 causes a novel polled and multisystemic syndrome in the progeny of a somatic mosaic bull

Author: Brigitte Marquant-Le Guienne, Hélène Hayes, Guy Noé, Cécile Grohs, Claire Ponsart, Laetitia Clément, Arnaud Delpeuch, Eric Pailhoux, Aurélie Auguste, Marie-Noelle Rossignol, Olivier Bouchez, Aurélien Capitan, Didier Boichard, Laura Salas-Cortes, Stéphane Chaffaux, Maëlle Pannetier, Sarah Barbey, Christophe Klopp, Cécile Donnadieu, Yves Gallard, Marie-Christine Deloche, Diane Esquerre, Harmonie Barasc, Daniel Le Bourhis, Dominique Dozias, Eric Venot, Stephan Bouet, Alain Pinton, Céline Chantry-Darmon, Emeline Lhuilier, Gerald Salin, Bernard Weiss, Emilie Cobo, Aurélie Allais-Bonnet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Département Recherche et Développement, Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, Département Génétique, Identification, Phénotypes et Systèmes d'Information en Elevage, Institut de l'Elevage, Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Domaine expérimental animal du Pin (SEA), Unité de Biométrie et Intelligence Artificielle (UBIA), This project was funded by Apis Gène 'Hornout' and INRA-DGA 'Hornaseq' grants., Biologie du développement et reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Institut de l'élevage (IDELE), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: Male, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, corne, Anatomy and Physiology, bovin, Somatic cell, Digestive Physiology, Inheritance Patterns, Skin Anatomy, lcsh:Medicine, Veterinary Anatomy and Physiology, Animal Digestive Anatomy, Cardiovascular, Cardiovascular System, Digestive Anatomy, Loss of heterozygosity, Animal Musculoskeletal Anatomy, Pregnancy, Reproductive Physiology, lcsh:Science, Base Pairing, Musculoskeletal System, Musculoskeletal Anatomy, Horns, Sequence Deletion, Skin, Genetics, 0303 health sciences, Multidisciplinary, Mosaicism, Congenital Heart Disease, Chromosome Mapping, Obstetrics and Gynecology, Embryo, Syndrome, 04 agricultural and veterinary sciences, Premature ovarian failure, Autosomal Dominant, symbols, Medicine, Female, Genital Anatomy, Research Article, Cattle Diseases, Locus (genetics), Gastroenterology and Hepatology, Biology, Real-Time Polymerase Chain Reaction, 03 medical and health sciences, symbols.namesake, Fetus, Animal Genital Anatomy, medicine, Animals, Humans, Abnormalities, Multiple, Gene, 030304 developmental biology, Clinical Genetics, lcsh:R, Reproductive System, 0402 animal and dairy science, Wild type, medicine.disease, 040201 dairy & animal science, Repressor Proteins, Animal Skin Anatomy, Mutation, Cardiovascular Anatomy, Mendelian inheritance, Cattle, Veterinary Science, lcsh:Q, Digestive System
Abstract: Polled and Multisystemic Syndrome (PMS) is a novel developmental disorder occurring in the progeny of a single bull. Its clinical spectrum includes polledness (complete agenesis of horns), facial dysmorphism, growth delay, chronic diarrhea, premature ovarian failure, and variable neurological and cardiac anomalies. PMS is also characterized by a deviation of the sex-ratio, suggesting male lethality during pregnancy. Using Mendelian error mapping and whole-genome sequencing, we identified a 3.7 Mb deletion on the paternal bovine chromosome 2 encompassing ARHGAP15, GTDC1 and ZEB2 genes. We then produced control and affected 90-day old fetuses to characterize this syndrome by histological and expression analyses. Compared to wild type individuals, affected animals showed a decreased expression of the three deleted genes. Based on a comparison with human Mowat-Wilson syndrome, we suggest that deletion of ZEB2, is responsible for most of the effects of the mutation. Finally sperm-FISH, embryo genotyping and analysis of reproduction records confirmed somatic mosaicism in the founder bull and male-specific lethality during the first third of gestation. In conclusion, we identified a novel locus involved in bovid horn ontogenesis and suggest that epithelial-to-mesenchymal transition plays a critical role in horn bud differentiation. We also provide new insights into the pathogenicity of ZEB2 loss of heterozygosity in bovine and humans and describe the first case of male-specific lethality associated with an autosomal locus in a non-murine mammalian species. This result sets PMS as a unique model to study sex-specific gene expression/regulation.
Published: 2012
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49. Pyroséquençage pour le développement d'EST et de SNP aviaires

Author: Frédérique Pitel, Alain Vignal, Sophie Leroux, Katia Feve, Florence Vignoles, Aurélie Tircazes, Mireille Morisson, Amandine Marty, Cécile Donnadieu, Denis Milan, David Gourichon, Francis Minvielle, Christine Leterrier, Cécile Arnould, Marie-Dominique Bernadet, Christel Marie-Etancelin, Benjamin Basso, Frédéric Herault, Frédéric Lecerf, Joël Besnard, Fanny Calenge, Catherine Beaumont, Christophe Klopp, Christian Diot, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Plateforme génomique fonctionnelle (PGFB), Université Bordeaux Segalen - Bordeaux 2, Pôle d'Expérimentation Avicole de Tours (UE PEAT), Institut National de la Recherche Agronomique (INRA), Génétique et Diversité Animales (GEDANIM), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Innovation et Développement dans l'Agriculture et l'Agro-alimentaire (UMR Innovation), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Palmipèdes à Foie Gras (UEPFG), Station d'Amélioration Génétique des Animaux (SAGA), Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Ecole Nationale Supérieure Agronomique de Rennes, Unité de Recherches Avicoles (URA), INRA, BIA-UR875, Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Pôle d'Expérimentation Avicole de Tours (PEAT), Innovation et Développement dans l'Agriculture et l'Agro-alimentaire (Innovation), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre national d'études agronomiques des régions chaudes (CNEARC)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), IFR140-Ecole Nationale Supérieure Agronomique de Rennes-AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), and INRA (UR83 Recherches Avicoles F-37380 Nouzilly, France)
Subjects: ARN, GENOME, CAILLE, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, SEQUENÇAGE, ADN, GALLUS DOMESTICUS, CANARD, MARQUEUR MOLECULAIRE, COTURNIX COTURNIX, POULE, ANSER DOMESTICUS
Abstract: Le but du programme est de combler les déficits en marqueurs observés pour trois espèces aviaires : la caille, le canard et la poule. La stratégie choisie est l'obtention, à partir de plusieurs individus de lignées d'intérêt, de SNP (Single Nucleotide Polymorphism, polymorphisme d'un nucléotide) par une nouvelle technologie de séquençage à haut débit (séquenceur 454 GS-FLX, Roche). Nous séquençons des représentations réduites du génome, en sélectionnant d'une part des fragments de restriction d'ADN génomique - les mêmes chez tous les individus - et d'autre part les transcrits qui représentent globalement la partie du génome correspondant aux gènes exprimés. Ces expérimentations sont réalisées à partir d'échantillons d'ADN ou d'ARN issus d'individus de lignées à l'origine de croisements existants, pour chacune des trois espèces. Les données générées par plusieurs "runs" de séquence seront traitées in silico : contigage à haut débit, recherche de SNP, comparaison avec les banques de séquences connues...En plus de l'intérêt que représente la production d'un très grand nombre de SNP nouveaux, cette technologie devrait permettre de mieux séquencer les régions riches en (G+C) correspondant aux plus petits des microchromosomes pour lesquels il n'y a pas de séquence chez la poule. La comparaison des séquences des transcrits obtenues chez la caille et le canard avec la séquence du génome de la poule permettra d'établir une "cartographie virtuelle" des SNP obtenus, grâce à la grande conservation de synténie existant entre ces trois espèces.
Published: 2009

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

Author: Stefan Kusch, Heba M. M. Ibrahim, Catherine Zanchetta, Celine Lopez-Roques, Cecile Donnadieu, and Sylvain Raffaele
Subjects: fungal pathogen, grass plants, genome, host specific, long read sequencing, Myriosclerotinia sulcatula, Microbiology, QR1-502, Botany, QK1-989
Abstract: The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.
Published: 2020
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