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2. A multi-omics dataset of the response to early plant polysaccharide ingestion in rabbits

Author

Charlotte Paës, Martin Beaumont, Thierry Gidenne, Karine Bébin, Joël Duperray, Charly Gohier, Emeline Guené-Grand, Gwénaël Rebours, Adrien Castinel, Céline Barilly, Béatrice Gabinaud, Carole Bannelier, Laure Gress, François Laperruque, Patrick Aymard, Anne-Marie Debrusse, Laurent Cauquil, Géraldine Pascal, and Sylvie Combes

Subjects
Science
Abstract

Abstract The transition from a milk-based diet to exclusive solid feeding deeply modifies microbiota-host crosstalk. Specifically, early ingestion of plant polysaccharides would be one of the main nutritional components to drive host-microbiota-interaction. To capture the effects of polysaccharides early-life nutrition (starch vs rapidly fermentable fiber) on the holobiont development, we investigated on the one hand the gut bacteriome and metabolome and on the other hand the transcriptome of two host gut tissues. Rabbit model was used to study post-natal co-development of the gut microbiota and its host around weaning transition. The assessment of the microbial composition of the gut appendix together with the caecum was provided for the first time. Gene expression signatures were analyzed along the gut (ileum and caecum) through high-throughput qPCR. The data collected were completed by the analysis of animal growth changes and time-series assessment of blood biomarkers. Those accessible and reusable data could help highlight the gut development dynamics as well as biological adaptation processes at the onset of solid feeding.

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. Early Introduction of Plant Polysaccharides Drives the Establishment of Rabbit Gut Bacterial Ecosystems and the Acquisition of Microbial Functions

Author

Charlotte Paës, Thierry Gidenne, Karine Bébin, Joël Duperray, Charly Gohier, Emeline Guené-Grand, Gwénaël Rebours, Céline Barilly, Béatrice Gabinaud, Laurent Cauquil, Adrien Castinel, Géraldine Pascal, Vincent Darbot, Patrick Aymard, Anne-Marie Debrusse, Martin Beaumont, and Sylvie Combes

Subjects
first food, gut health, gut microbiota, intestinal development, metabolomics, microbiota development, Microbiology, QR1-502
Abstract

ABSTRACT In mammals, the introduction of solid food is pivotal for the establishment of the gut microbiota. However, the effects of the first food consumed on long-term microbiota trajectory and host response are still largely unknown. This study aimed to investigate the influences of (i) the timing of first solid food ingestion and (ii) the consumption of plant polysaccharides on bacterial community dynamics and host physiology using a rabbit model. To modulate the first exposure to solid nutrients, solid food was provided to suckling rabbits from two different time points (3 or 15 days of age). In parallel, food type was modulated with the provision of diets differing in carbohydrate content throughout life: the food either was formulated with a high proportion of rapidly fermentable fibers (RFF) or was starch-enriched. We found that access to solid food as of 3 days of age accelerated the gut microbiota maturation. Our data revealed differential effects according to the digestive segment: precocious solid food ingestion influenced to a greater extent the development of bacterial communities of the appendix vermiformis, whereas life course polysaccharides ingestion had marked effects on the cecal microbiota. Greater ingestion of RFF was assumed to promote pectin degradation as revealed by metabolomics analysis. However, transcriptomic and phenotypic host responses remained moderately affected by experimental treatments, suggesting little outcomes of the observed microbiome modulations on healthy subjects. In conclusion, our work highlighted the timing of solid food introduction and plant polysaccharides ingestion as two different tools to modulate microbiota implantation and functionality. IMPORTANCE Our study was designed to gain a better understanding of how different feeding patterns affect the dynamics of gut microbiomes and microbe–host interactions. This research showed that the timing of solid food introduction is a key component of the gut microbiota shaping in early developmental stages, though with lower impact on settled gut microbiota profiles in older individuals. This study also provided in-depth analysis of dietary polysaccharide effects on intestinal microbiota. The type of plant polysaccharides reaching the gut through the lifetime was described as an important modulator of the cecal microbiome and its activity. These findings will contribute to better define the interventions that can be employed for modulating the ecological succession of young mammal gut microbiota.

Published
2022
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9. Science diplomacy for plant health

Author

Giovani, Baldissera, Blümel, Sylvia, Lopian, Ralf, Teulon, David, Bloem, Stephanie, Galeano Martínez, Cristina, Beltrán Montoya, Camilo, Urias Morales, Carlos Ramon, Dharmapuri, Sridhar, Timote, Visoni, Horn, Nico, Chouibani, Mekki, Mezui M’Ella, Jean Gérard, Herrera, Veronica, Castinel, Aurélie, Goletsos, Con, Moeller, Carina, Naumann, Ian, Stancanelli, Giuseppe, Bronzwaer, Stef, Tramontini, Sara, MacDonald, Philip, Matheson, Loren, Anthoine, Géraldine, De Jonghe, Kris, Schenk, Martijn, Steinmöller, Silke, Rodriguez, Elena, Cruz, Maria Leonor, Luck, Jo, Fraser, Greg, Brunel, Sarah, Montuori, Mirko, Fedchock, Craig, Steel, Elspeth, Pennington, Helen Grace, Day, Roger, Rossi, Jean Pierre, and Xia, Jingyuan

Published
2020
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12. Leg Posterior Muscle Compartment Injuries

Author

Delaunay, Francois, Adam, Philippe, Castinel, Bernard, Auriol, Julien, Roger, Bernard, Landreau, Philippe, Series editor, Roger, Bernard, editor, Guermazi, Ali, editor, and Skaf, Abdalla, editor

Published
2017
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13. A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling

Author

Eché, Camille, primary, Iampietro, Carole, additional, Birbes, Clément, additional, Dréau, Andreea, additional, Kuchly, Claire, additional, Di Franco, Arnaud, additional, Klopp, Christophe, additional, Faraut, Thomas, additional, Djebali, Sarah, additional, Castinel, Adrien, additional, Zytnicki, Matthias, additional, Denis, Erwan, additional, Boussaha, Mekki, additional, Grohs, Cécile, additional, Boichard, Didier, additional, Gaspin, Christine, additional, Milan, Denis, additional, and Donnadieu, Cécile, additional

Published
2023
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14. 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

15. A carvacrol-based product reduces Campylobacter jejuni load and alters microbiota composition in the caeca of chickens

Author

Allaoua, Marion, Bonnafé, Elsa, Etienne, Pierre, Noirot, Virginie, Gabarrou, Jean-François, Castinel, Adrien, Pascal, Géraldine, Darbot, Vincent, Treilhou, Michel, Combes, Sylvie, Gabarrou, Jean‐François, Laboratoires Phodé, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), 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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), and 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)

Subjects
feed additive, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, animal diseases, Microbiota, digestive, oral, and skin physiology, food and beverages, microbiome, 16Sr RNA gene sequencing, General Medicine, bacterial infections and mycoses, foodborne disease, digestive system, Applied Microbiology and Biotechnology, essential oil, Campylobacter jejuni, broiler chicken, RNA, Ribosomal, 16S, Campylobacter Infections, Animals, Cymenes, PICRUSt2, Cecum, Chickens, Poultry Diseases, Biotechnology
Abstract

Aim This study was conducted to test the ability of a carvacrol-based formulation (Phodé, France) to decrease the C. jejuni caecal load in inoculated broiler chickens and to study the impact of the C. jejuni inoculation alone or combined with the product, on the caecal microbiota. Methods and Results On day 1, chickens were either fed a control feed or the same diet supplemented with a carvacrol-based product. On day 21, the carvacrol-supplemented chickens and half of the non-supplemented chickens were inoculated with C. jejuni (108 CFU). Quantitative PCR was used to quantify C. jejuni in chicken caecal samples and 16S rRNA gene sequencing was carried out at 25, 31 and 35 days of age. A significant decrease of 1.4 log of the C. jejuni caecal load was observed in 35-day-old chickens supplemented with the product, compared to the inoculated and unsupplemented group (p < 0.05). The inoculation with C. jejuni significantly increased the population richness, Shannon and Simpson diversity and altered beta-diversity. Compared to the control group, the C. jejuni inoculation causes significant changes in the microbiota. The carvacrol-based product associated with C. jejuni inoculation increased the diversity and strongly modified the structure of the microbial community. Functional analysis by 16S rRNA gene-based predictions further revealed that the product up-regulated the pathways involved in the antimicrobial synthesis, which could explain its shaping effect on the caecal microbiota. Conclusions Our study confirmed the impairment of the caecal bacterial community after inoculation and demonstrated the ability of the product to reduce the C. jejuni load in chickens. Further investigations are needed to better understand the mode of action of this product to promote the installation of a beneficial microbiota to its host. Significance and Impact of the Study Results suggested that this product could be promising to control C. jejuni contamination of broilers.

Published
2022

18. French multicentre prospective evaluation of radiofrequency ablation in the management of haemorrhoidal disease

Author

A. Laurain, D. Bouchard, J.-M. Rouillon, P. Petit, A. Liddo, B. Vinson Bonnet, A. Venara, J.-M. Didelot, G. Bonnaud, A. Senéjoux, T. Higuero, P. Delasalle, A.-L. Tarrerias, F. Devulder, A. Castinel, C. Thomas, H. Pillant Le Moult, C. Favreau-Weltzer, and L. Abramowitz

Subjects
Gastroenterology, Surgery
Abstract

Purpose The aim of this study was to evaluate the efficacy and safety of radiofrequency ablation (RFA) in the management of haemorrhoidal disease with 1 year’s follow-up. Method This prospective multicentre study assessed RFA (Rafaelo©) in outpatients with grade II–III haemorrhoids. RFA was performed in the operating room under locoregional or general anaesthesia. Primary endpoint was the evolution of a quality-of-life score adapted to the haemorrhoid pathology (HEMO-FISS-QoL) 3 months after surgery. Secondary endpoints were evolution of symptoms (prolapsus, bleeding, pain, itching, anal discomfort), complications, postoperative pain and medical leave. Results A total of 129 patients (69% men, median age 49 years) were operated on in 16 French centres. Median HEMO-FISS-QoL score dropped significantly from 17.4/100 to 0/100 (p p p p Conclusion RFA is associated with an improvement in quality of life and symptoms with a good safety profile. As expected for minimally invasive surgery, postoperative pain is minor with short medical leave. Clinical trial registration and date Clinical trial NCT04229784 (18/01/2020).

Published
2023

19. Genome structures resolve the early diversification of teleost fishes

Author

Parey, Elise, primary, Louis, Alexandra, additional, Montfort, Jerome, additional, Bouchez, Olivier, additional, Roques, Céline, additional, Iampietro, Carole, additional, Lluch, Jerome, additional, Castinel, Adrien, additional, Donnadieu, Cécile, additional, Desvignes, Thomas, additional, Floi Bucao, Christabel, additional, Jouanno, Elodie, additional, Wen, Ming, additional, Mejri, Sahar, additional, Dirks, Ron, additional, Jansen, Hans, additional, Henkel, Christiaan, additional, Chen, Wei-Jen, additional, Zahm, Margot, additional, Cabau, Cédric, additional, Klopp, Christophe, additional, Thompson, Andrew W., additional, Robinson-Rechavi, Marc, additional, Braasch, Ingo, additional, Lecointre, Guillaume, additional, Bobe, Julien, additional, Postlethwait, John H., additional, Berthelot, Camille, additional, Roest Crollius, Hugues, additional, and Guiguen, Yann, additional

Published
2023
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20. 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

22. Transport to the Slaughterhouse Affects the Salmonella Shedding and Modifies the Fecal Microbiota of Finishing Pigs

Author

Francesca Romana Massacci, Alessandra Morelli, Lucilla Cucco, Adrien Castinel, Roberta Ortenzi, Silvia Tofani, Giovanni Pezzotti, Jordi Estellé, Marta Paniccià, and Chiara Francesca Magistrali

Subjects
swine, infection, Salmonella, intestinal composition, Veterinary medicine, SF600-1100, Zoology, QL1-991
Abstract

Contaminated pork is a significant source of foodborne Salmonellosis. Pork is contaminated at the slaughterhouse and the intestinal content is the predominant source of Salmonella for carcass contamination. The prevalence of Salmonella-positive pigs increases significantly when the time of transport to the slaughterhouse is longer than two hours. The hypothesis behind this study is that transport to the slaughterhouse increases the load of Salmonella in feces and determines a shift of the fecal microbiota in finishing pigs. Fecal samples were collected in a pig herd positive for Salmonella spp., the day before the transport and at the slaughterhouse. Salmonella loads were estimated by the most probable number (MPN) technique, according to the ISO/TS 6579-2:2012/A1. Moreover, the fecal bacteria composition was assessed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Our study showed that the load of Salmonella increases after transport, confirming that this phase of the production chain is a critical point for the control of Salmonella contamination. A lower richness and an increased beta-diversity characterized the fecal microbiota composition of Salmonella-positive animals after transport. In this stage, a natural Salmonella infection causes a disruption of the fecal microbiota as observed in challenge studies.

Published
2020
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23. Publisher Correction: Science diplomacy for plant health

Author

Giovani, Baldissera, Blümel, Sylvia, Lopian, Ralf, Teulon, David, Bloem, Stephanie, Galeano Martínez, Cristina, Beltrán Montoya, Camilo, Urias Morales, Carlos Ramon, Dharmapuri, Sridhar, Timote, Visoni, Horn, Nico, Chouibani, Mekki, Mezui M’Ella, Jean Gérard, Herrera, Veronica, Castinel, Aurélie, Goletsos, Con, Moeller, Carina, Naumann, Ian, Stancanelli, Giuseppe, Bronzwaer, Stef, Tramontini, Sara, MacDonald, Philip, Matheson, Loren, Anthoine, Géraldine, De Jonghe, Kris, Schenk, Martijn, Steinmöller, Silke, Rodriguez, Elena, Cruz, Maria Leonor, Luck, Jo, Fraser, Greg, Brunel, Sarah, Montuori, Mirko, Fedchock, Craig, Steel, Elspeth, Pennington, Helen Grace, Day, Roger, Rossi, Jean Pierre, and Xia, Jingyuan

Published
2020
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24. Apport de l’étude des fonctions des cellules NK dans le diagnostic biologique de la lymphohistiocytose hémophagocytaire héréditaire

Author

Castinel, Lola, Aix-Marseille Université - Faculté de pharmacie (AMU PHARM), Aix Marseille Université (AMU), and Frédéric Vely

Subjects
Cytotoxicité, [SDV]Life Sciences [q-bio], [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, Cellules NK, Dégranulation, Lymphohistiocytose hémophagocytaire héréditaire
Abstract

La lymphohistiocytose hémophagocytaire familiale (LHF) est une entité clinique-biologique-histologique rare due à un défaut d’homéostasie du système immunitaire caractérisée par une hyperactivation des lymphocytes et des histiocytes. Étant donné son taux de mortalité élevé, il s’agit d’une urgence diagnostique et thérapeutique. L’étude des gènes responsables de la HLH a permis de caractériser ses différents sous types et de faciliter son diagnostic. Cependant, le rendu des résultats de génétique peut être long, d’où l’intérêt du développement de tests de dépistage diagnostique plus rapides, comme les tests fonctionnels des cellules NK. Ces analyses permettant d’évaluer leur activité sont les tests de dégranulation, l’analyse de l’expression de la perforine et la cytotoxicité lymphocytaire.Actuellement, ces tests biologiques d’aide au diagnostic se font par cytométrie en flux sur des cellules mononuclées du sang périphérique (PBMC) isolées du sang du patient par séparation sur gradient de Ficoll et incubées dans différents milieux. La stimulation des cellules NK est réalisée avec des cellules cibles (cellules K562 et P815 recouvertes d’anticorps anti-P815). Ces tests d’exploration fonctionnelle des cellules NK se sont montrés pertinents pour les 8 patients présentés, avec selon les cas, des anomalies de l’expression de la perforine ou de la capacité à dégranuler des cellules NK.Au vu du caractère urgent du diagnostic, il est important d’avoir un test prêt à l’emploi réalisable dans le cadre d’une routine hospitalière capable de s’affranchir des cultures de lignées : la mise en place de ce test est en cours au laboratoire.

Published
2022

25. The benefits of long read HiFi sequencing for metabarcoding analysis

Author

Castinel, Adrien, Mainguy, Jean, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Hoede, Claire, Pascal, Géraldine, Bouchez, Olivier, and Castinel, Adrien

Subjects
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
Abstract

Today, the variable regions of 16S rRNA gene (V3-V4) is widely used to profile microbial communities, however the limited read lengths (460pb for the V3-V4 region) combined with the complexity of microbial samples makes it difficult to accurately identify bacterial strains and their abundance.The arrival PacBio Sequel II allow us to generate longer reads named “HiFi reads” using the circular consensus sequencing (CCS) mode, with an accuracy similar to the one observed on short reads. Therefore, we wanted to evaluate the taxonomic resolution using longer target region sequencing, such as, the full-length 16S (1.5kb) and 16S-23S genes (operon 4.5kb) and compared them to 16S RNA V3-V4 region. First, we have evaluated and implemented an extraction method in order to produce high size DNA fragment for long read sequencing while maintaining a good representativeness.Then, we conducted a comparative study of three PacBio protocols, the “Barcoded universal primers protocol” (BUP), the “Barcoded target specific primers protocol” (BTSP) and the “Barcoded overhang adapters protocol” (BOA) in order to perform CCS sequencing of the 16S, and 16S-23S genes on a microbial Community standard (mock) as well as pig faeces samples. Finally, we compared the taxonomic resolution between the 16S-23S, the 16S full length, and the 16sRNA V3V4. This work have been carried out within the framework of the SeqOccIn project (Sequencing Occitanie Innovation), supported by Get-PlaGe and Genotoul Bioinfo core facilities and financed by FEDER funds (Programme Opérationnel FEDER-FSE_Midi-Pyrénées et Garonne 2014-2020).

Published
2022

28. metagWGS: a workflow to analyse short and long HiFi metagenomic reads Taxonomic profile HiFi vs Short reads assembly

Author

Fourquet, Joanna, Mainguy, Jean, Vienne, Maïna, Noirot, Céline, Martin, Pierre, Darbot, Vincent, Bouchez, Olivier, Castinel, Adrien, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Pascal, Géraldine, Hoede, Claire, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Bio-Informatique - Génotoul, Université Fédérale Toulouse Midi-Pyrénées, 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), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), 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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Société Française de Bioinformatique, GDR Bioinformatique Moléculaire, Institut Français de Bioinformatique, Institut national de recherche en sciences et technologies du numérique, FEDER funds (Programme Opérationnel FEDER-FSE_Midi-Pyrénées et Garonne 2014-2020), ATB_Biofilm funded by PNREST Anses, 2020/01/142, and Hoede, Claire

Subjects
bioInfOmics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience

Published
2022

29. Early Introduction of Plant Polysaccharides Drives the Establishment of Rabbit Gut Bacterial Ecosystems and the Acquisition of Microbial Functions

Author

Paës, Charlotte, primary, Gidenne, Thierry, additional, Bébin, Karine, additional, Duperray, Joël, additional, Gohier, Charly, additional, Guené-Grand, Emeline, additional, Rebours, Gwénaël, additional, Barilly, Céline, additional, Gabinaud, Béatrice, additional, Cauquil, Laurent, additional, Castinel, Adrien, additional, Pascal, Géraldine, additional, Darbot, Vincent, additional, Aymard, Patrick, additional, Debrusse, Anne-Marie, additional, Beaumont, Martin, additional, and Combes, Sylvie, additional

Published
2022
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30. Avancées réalisées en métabarcoding et en métagénomique dans le cadre du projet SeqOccIn grâce au séquençage longs fragments

Author

Milan, Denis, Mainguy, Jean, Castinel, Adrien, Bouchez, Olivier, Combes, Sylvie, Hoede, Claire, Pascal, Géraldine, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Plateforme Bio-Informatique - Génotoul, Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), 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 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 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), and Pascal, Géraldine

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

National audience

Published
2022

31. 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

Wen, Ming, primary, Pan, Qiaowei, additional, Jouanno, Elodie, additional, Montfort, Jerome, additional, Zahm, Margot, additional, Cabau, Cédric, additional, Klopp, Christophe, additional, Iampietro, Carole, additional, Roques, Céline, additional, Bouchez, Olivier, additional, Castinel, Adrien, additional, Donnadieu, Cécile, additional, Parrinello, Hugues, additional, Poncet, Charles, additional, Belmonte, Elodie, additional, Gautier, Véronique, additional, Avarre, Jean‐Christophe, additional, Dugue, Remi, additional, Gustiano, Rudhy, additional, Hà, Trần Thị Thúy, additional, Campet, Marc, additional, Sriphairoj, Kednapat, additional, Ribolli, Josiane, additional, de Almeida, Fernanda L., additional, Desvignes, Thomas, additional, Postlethwait, John H., additional, Bucao, Christabel Floi, additional, Robinson‐Rechavi, Marc, additional, Bobe, Julien, additional, Herpin, Amaury, additional, and Guiguen, Yann, additional

Published
2022
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32. Genome structures resolve the early diversification of teleost fishes

Author

Parey, Elise, primary, Louis, Alexandra, additional, Montfort, Jerome, additional, Bouchez, Olivier, additional, Roques, Céline, additional, Iampietro, Carole, additional, Lluch, Jerome, additional, Castinel, Adrien, additional, Donnadieu, Cécile, additional, Desvignes, Thomas, additional, Bucao, Christabel Floi, additional, Jouanno, Elodie, additional, Wen, Ming, additional, Mejri, Sahar, additional, Dirks, Ron, additional, Jansen, Hans, additional, Henkel, Christiaan, additional, Chen, Wei-Jen, additional, Zahm, Margot, additional, Cabau, Cédric, additional, Klopp, Christophe, additional, Thompson, Andrew W., additional, Robinson-Rechavi, Marc, additional, Braasch, Ingo, additional, Lecointre, Guillaume, additional, Bobe, Julien, additional, Postlethwait, John H., additional, Berthelot, Camille, additional, Crollius, Hugues Roest, additional, and Guiguen, Yann, additional

Published
2022
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33. 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

34. Male gender is associated with informal caregiver burden in patients with chronic intestinal failure treated with home parenteral nutrition

Author

Jean Castinel, Gauthier Pellet, David Laharie, Frank Zerbib, Christine Silvain, Eva Wilsius, Laurianne Kerlogot, Pauline Rivière, and Florian Poullenot

Subjects
Male, Nutrition and Dietetics, Medicine (miscellaneous), Caregiver Burden, Middle Aged, Intestinal Failure, Intestinal Diseases, Caregivers, Chronic Disease, Quality of Life, Humans, Female, Prospective Studies, Parenteral Nutrition, Home
Abstract

Home parenteral nutrition (HPN) is the recommended treatment in patients with chronic intestinal failure (CIF). HPN is associated with a worsening of patients' quality of life and has a dramatic impact on personal and familial daily life. Little is known about the informal caregiver burden of patients receiving HPN.To assess informal caregiver burden and the factors associated with moderate-to-severe caregiver burden in patients treated with HPN.Informal caregivers of consecutive patients treated with HPN in a French nutrition referral center were invited to participate in a survey between January 2021 and June 2021. They had to fill out an anonymous standardized self-questionnaire evaluating burden by the Zarit Burden Interview (ZBI) and depression and anxiety symptoms by the Hospital Anxiety and Depression Scale (HADS) score since HPN introduction.Among the 87 HPN patients having informal caregivers, 53 (61%) completed the questionnaire. Thirty (57%) informal caregivers were women. The caregiver's median age was 62 years (IQR, 21.0). Twelve (22%) expressed moderate to severe burden (ZBI score, 41-88). In a multivariate analysis, the caregiver's male gender (odds ratio [OR], 16.45; 95% CI, 2.30-238.75; P = 0.014) and the number of simultaneous infusions per day1 (OR, 9.92; 95% CI, 1.35-121.60; P = 0.0038) were associated with a moderate to severe burden. Twenty caregivers reported anxious and depressive symptoms with an elevated HADS score.In this prospective survey, a minority of informal caregivers of patients with CIF being treated with HPN expressed moderate to severe burden. The caregiver's male gender was associated with a higher burden in patients with CIF.

Published
2022

35. Implementation of new methods for metagenomics analysis using PacBio HiFi sequencing

Author

Castinel, Adrien, Mainguy, Jean, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Hoede, Claire, Pascal, Géraldine, Bouchez, Olivier, and iampietro, carole

Subjects
[SDV] Life Sciences [q-bio], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

The variable regions of 16S rRNA gene is widely used to profile microbial communities, however the limited read lengths (e.g 460pb for the V3-V4 region) combined with the complexity of microbial samples makes it difficult to accurately identify bacterial strains and their abundance. The arrival PacBio Sequel II sequencer allow us to generate longer reads named "HiFi reads" using the circular consensus sequencing (CCS) mode, with an accuracy similar to the one observed for short reads sequencers.

Published
2022

36. metagWGS: a workflow to analyse short and long HiFi metagenomic reads

Author

Fourquet, Joanna, Vienne, Maïna, Mainguy, Jean, Darbot, Vincent, Martin, Pierre, Bouchez, Olivier, Castinel, Adrien, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Noirot, Céline, Pascal, Géraldine, Hoede, Claire, Hoede, Claire, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), 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), 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), Plateforme Bio-Informatique - Génotoul, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), 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), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience

Published
2022

37. Strengths and limits of long read metabarcoding

Author

Mainguy, Jean, Castinel, Adrien, Bouchez, Olivier, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Hoede, Claire, Pascal, Géraldine, and Pascal, Géraldine

Subjects
16-23S, metabarcoding, HiFi long reads, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Metabarcoding is the large-scale taxonomic identification of complex environmental samples via analysis of DNA reads of one marker gene. Different marker genes are used, the 16S rRNA gene is mainly used to identify bacteria. We conducted a comparative study to understand the limitations and strengths of PacBio HiFi long read sequencing technology for metabarcoding analyses. We performed the same analyses on two types of datasets. A commercial ZymoBIOMICS mock community consisting of eight bacteria and 32 samples containing pig fecal microbiota from the ExpomycoPig project. We focused on the 16S-23S rRNA gene operon and sequenced 3 types of amplicons by metabarcoding: the V3-V4 region of the 16S rRNA, the full-length 16S rRNA gene and the full-length 16S-23S gene operon. We observe that by using HIFI long reads we increase the specificity of sample characterization. But when we analyze the 16S-23S amplicons, the specificity increases within the limit of the availability of the sequence in the databases that are much less comprehensive than the databases containing only 16S data. A strategy of affiliating 16S-23S amplicons on complementary databases (Silva 16S and 23S and a custom 16S-23S operon database) improves microbial identifications.

Published
2022

41. Influência da saúde periodontal na performance do atleta de alta competição: revisão integrativa da literatura

Author

Castinel, Lucien Paul Pierre and Castro, Filipe

Subjects
Ciências Médicas::Medicina Clínica [Domínio/Área Científica], Sports performance, Periodontal health, Profissional athlete
Abstract

Submitted by Ana Moreira (anadsmoreira@ufp.pt) on 2022-02-02T13:11:36Z No. of bitstreams: 1 PPG_36437.pdf: 992349 bytes, checksum: bf91c0e59d4b54da0b1ecf0ba54db9f4 (MD5) Approved for entry into archive by azevedo@ufp.pt (azevedo@ufp.pt) on 2022-02-03T12:18:44Z (GMT) No. of bitstreams: 1 PPG_36437.pdf: 992349 bytes, checksum: bf91c0e59d4b54da0b1ecf0ba54db9f4 (MD5) Made available in DSpace on 2022-02-03T12:18:44Z (GMT). No. of bitstreams: 1 PPG_36437.pdf: 992349 bytes, checksum: bf91c0e59d4b54da0b1ecf0ba54db9f4 (MD5) Previous issue date: 2021-09-29

Published
2021

42. 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

44. Host genotype and amoxicillin administration affect the incidence of diarrhoea and faecal microbiota of weaned piglets during a natural multiresistant ETEC infection

Author

Silvia Tofani, Claudio Forte, Gaetan Lemonnier, Adrien Castinel, Claudia Bevilacqua, Claire Rogel-Gaillard, Chiara Francesca Magistrali, Lucia Marchi, Giovanni Pezzotti, Carmela Lovito, Diana Luise, Micol Bertocchi, Serenella Orsini, Paolo Trevisi, Fany Blanc, Jordi Estellé, Michele Tentellini, Francesca Romana Massacci, Francesca Romana Massacci,| Silvia Tofani, Claudio Forte, Micol Bertocchi, Carmela Lovito, Serenella Orsini, Michele Tentellini, Lucia Marchi, Gaetan Lemonnier, Diana Luise, Fany Blanc, Adrien Castinel, Claudia Bevilacqua, Claire Rogel‐Gaillard, Giovanni Pezzotti, Jordi Estellé, Paolo Trevisi, Chiara Francesca Magistrali, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Partenaires INRAE, Department of Agricultural and Food Sciences, University of Bologna, Génétique Animale et Biologie Intégrative (GABI), 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), 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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ministry of Health, ItalyIZSUM RC 006/2016INRA (Animal Genetics division)France Genomique National infrastructureANR-10INBS-09Department of Agricultural and Food Sciences (DISTAL) of Bologna University (Italy), Université Paris-Saclay-AgroParisTech-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), 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)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)

Subjects
Antibiotic resistance, Swine, [SDV]Life Sciences [q-bio], Antibiotics, Gut flora, medicine.disease_cause, Feces, fluids and secretions, Food Animals, Oral administration, Enterotoxigenic Escherichia coli, Genotype, Escherichia coli Infections, 0303 health sciences, biology, Microbiota, Bacterial, Antibiotic resistance, Escherichia coli, FUT1, gut microbiota, MUC4, swine, General Medicine, Single Nucleotide, 3. Good health, medicine.drug, DNA, Bacterial, Diarrhea, medicine.drug_class, FUT1, Weaning, Polymorphism, Single Nucleotide, digestive system, Microbiology, 03 medical and health sciences, medicine, Escherichia coli, Animals, Polymorphism, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, gut microbiota, 030306 microbiology, Amoxicillin, DNA, biology.organism_classification, bacterial infections and mycoses, MUC4, swine, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Animal Science and Zoology
Abstract

International audience; Enterotoxigenic Escherichia coli (ETEC) is the aetiological agent of postweaning diarrhoea (PWD) in piglets. The SNPs located on the Mucine 4 (MUC4) and Fucosyltransferase 1 (FUT1) genes have been associated with the susceptibility to ETEC F4 and ETEC F18, respectively. The interplay between the MUC4 and FUT1 genotypes to ETEC infection and the use of amoxicillin in modifying the intestinal microbiota during a natural infection by multiresistant ETEC strains have never been investigated. The aim of this study was to evaluate the effects of the MUC4 and FUT1 genotypes and the administration of amoxicillin through different routes on the presence of diarrhoea and the faecal microbiota composition in piglets naturally infected with ETEC. Seventy-one piglets were divided into three groups: two groups differing by amoxicillin administration routes-parenteral (P) or oral (O) and a control group without antibiotics (C). Faecal scores, body weight, presence of ETEC F4 and F18 were investigated 4 days after the arrival in the facility (T0), at the end of the amoxicillin administration (T1) and after the withdrawal period (T2). The faecal bacteria composition was assessed by sequencing the 16S rRNA gene. We described that MUC4 and FUT1 genotypes were associated with the presence of ETEC F4 and ETEC F18. The faecal microbiota was influenced by the MUC4 genotypes at T0. We found the oral administration to be associated with the presence of diarrhoea at T1 and T2. Furthermore, the exposure to amoxicillin resulted in significant alterations of the faecal microbiota. Overall, MUC4 and FUT1 were confirmed as genetic markers for the susceptibility to ETEC infections in pigs. Moreover, our data highlight that group amoxicillin treatment may produce adverse outcomes on pig health in course of multiresistant ETEC infection. Therefore, alternative control measures able to maintain a healthy faecal microbiota in weaners are recommended.

Published
2020

45. A supernumerary “B-sex” chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus

Author

Imarazene, Boudjema, primary, Du, Kang, additional, Beille, Séverine, additional, Jouanno, Elodie, additional, Feron, Romain, additional, Pan, Qiaowei, additional, Torres-Paz, Jorge, additional, Lopez-Roques, Céline, additional, Castinel, Adrien, additional, Gil, Lisa, additional, Kuchly, Claire, additional, Donnadieu, Cécile, additional, Parrinello, Hugues, additional, Journot, Laurent, additional, Cabau, Cédric, additional, Zahm, Margot, additional, Klopp, Christophe, additional, Pavlica, Tomáš, additional, Al-Rikabi, Ahmed, additional, Liehr, Thomas, additional, Simanovsky, Sergey A., additional, Bohlen, Joerg, additional, Sember, Alexandr, additional, Perez, Julie, additional, Veyrunes, Frédéric, additional, Mueller, Thomas D., additional, Postlethwait, John H., additional, Schartl, Manfred, additional, Herpin, Amaury, additional, Rétaux, Sylvie, additional, and Guiguen, Yann, additional

Published
2021
Full Text
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46. Fissure anale

Author

Higuero, T., Didelot, J.-M., Castinel, A., Gompel, M., Rouillon, J.-M., Garros, A., and Tarrerias, A.-L.

Published
2017
Full Text
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48. The impacts of ostreid herpesvirus 1 microvariants on Pacific oyster aquaculture in the Northern and Southern Hemispheres since 2008

Author

R.J. Whittington, A. Castinel, D. Cheslett, D. Furones Nozal, and M. Fuhrmann

Subjects
0301 basic medicine, biology, business.industry, Biosecurity, Outbreak, General Medicine, Ostreid herpesvirus 1, 010501 environmental sciences, Pacific oyster, biology.organism_classification, 01 natural sciences, Fishery, 03 medical and health sciences, 030104 developmental biology, Geography, Aquaculture, Agriculture, Crassostrea, Epizootic disease, Animal Science and Zoology, business, 0105 earth and related environmental sciences
Abstract

Mollusc farming is the third most productive aquaculture activity in the world, and the Pacific oyster (Crassostrea gigas) is one of the most important farmed species. Since 2008, mass mortalities in C. gigas due to ostreid herpesvirus 1 microvariants have challenged the viability of this industry in Europe, New Zealand and Australia. Ten years after the emergence of this disease, there is evidence that the industry has become consolidated into fewer, larger companies, with the displacement of small farming enterprises and loss of employment in coastal communities. Rather than seeking technical solutions, the industry has turned to compensatory production strategies, such as increasing the number of spat placed on farms, higher market prices for table oysters and direct marketing, which appear to have allowed profitability. Biosecurity policies and responses to outbreaks, including those from within the industry, have had unintended consequences for hatcheries and farmers in areas free of disease, mainly caused by restrictions on animal movements, and have not prevented global spread. There may be opportunities for better coordination of industry and government responses to epizootic disease emergence in aquaculture. There is certainly a need for increased adoption of technical advances from research, once these solutions have been adequately verified.

Published
2019

49. Disease threats to farmed green-lipped mussels Perna canaliculus in New Zealand: review of challenges in risk assessment and pathway analysis

Author

A. Castinel, E. J. Peeler, S. C. Webb, J.B. Jones, and Barrie M. Forrest

Subjects
0106 biological sciences, Range (biology), Biosecurity, Disease, Management, Monitoring, Policy and Law, Aquatic Science, 01 natural sciences, lcsh:Aquaculture. Fisheries. Angling, lcsh:QH540-549.5, Perna canaliculus, Shellfish, Risk management, Water Science and Technology, lcsh:SH1-691, biology, Ecology, business.industry, 010604 marine biology & hydrobiology, 04 agricultural and veterinary sciences, Mussel, biology.organism_classification, 040102 fisheries, 0401 agriculture, forestry, and fisheries, lcsh:Ecology, business, Risk assessment, human activities
Abstract

The endemic green-lipped mussel (GLM) Perna canaliculus is a key cultural and economic species for New Zealand. Unlike other cultured shellfish species, GLMs have experienced relatively few disease issues. The apparent absence of diseases in both wild and farmed GLM populations does not preclude risks from environmental changes or from the introduction of overseas mussel pathogens and parasites. Potential for disease exchange between the GLM and other mytilid species present in New Zealand has yet to be elucidated. After reviewing and discussing relevant scientific literature, we present an initial assessment of GLM vulnerability to disease threats and the potential risk pathways for mussel pathogens and parasites into New Zealand and highlight a number of challenges. These include knowledge gaps relevant to GLM susceptibility to exotic pathogens and parasites, risk pathways into New Zealand and biosecurity risk associated with domestic pathways. Considerations and findings could potentially apply to other farmed aquatic species with limited distribution range and/or low disease exposure.

Published
2019

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