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2. Tissue Resources for the Functional Annotation of Animal Genomes

Author

Tixier-Boichard, Michèle, Fabre, Stéphane, Dhorne-Pollet, Sophie, Goubil, Adeline, Acloque, Hervé, Vincent-Naulleau, Silvia, Ross, Pablo, Wang, Ying, Chanthavixay, Ganrea, Cheng, Hans, Ernst, Catherine, Leesburg, Vicki, Giuffra, Elisabetta, Zhou, Huaijun, Group, Collaborative Working, Taragnat, Catherine, Berri, Cecile, Jardet, Déborah, Godet, Estelle, Laurent, Fabrice, Gomot, Gilles, Dardente, Hughes, Grasseau, Isabelle, Dubois, Jean-Philippe, Gautron, Joel, Gérard, Nadine, Quéré, Pascale, Lavocat, Roger-Paul, Dalbies-Tran, Rozenn, Métayer, Sonia, Marthey, Sylvain, Coustham, Vincent, and Druart, Xavier

Subjects
Biological Sciences, Genetics, tissue sampling, repository, mammals, bird, cryopreservation, genome, Collaborative Working Group, Clinical Sciences, Law
Abstract

In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, fat depot, skin, muscle, and peripheral blood mononuclear cells); set 2 comprises tissues requiring special protocols because of their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive tract, immune tissues, cartilage); set 3 comprises specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols were established and uploaded in https://data.faang.org/protocol/samples. Specificities between mammals and chicken are described when relevant. A total of 73 different tissues or tissue sections were collected, and 21 are common to the four species. Having a common set of tissues will facilitate the transfer of knowledge within and between species and will contribute to decrease animal experimentation. Combining data on the same samples will facilitate data integration. Quality control was performed on some tissues with RNA extraction and RNA quality control. More than 5,000 samples have been stored with unique identifiers, and more than 4,000 were uploaded onto the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement FAANG assays, with published results. All samples are available without restriction for further assays. The requesting procedure is described. Members of FAANG are encouraged to apply a range of molecular assays to characterize the functional status of collected samples and share their results, in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

Published
2021

6. Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaelle, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali San, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard-Van der Laan, Marie-Hélène, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Published
2019
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7. Bioinformatic Mining and Structure-Activity Profiling of Baeyer-Villiger Monooxygenases from Mycobacterium tuberculosis

Author

Tomas, Nicolas, primary, Leonelli, Dimitri, additional, Campoy, Martin, additional, Marthey, Sylvain, additional, Le, Nguyen-Hung, additional, Rengel, David, additional, Martin, Véronique, additional, Pál, Adrian, additional, Korduláková, Jana, additional, Eynard, Nathalie, additional, Guillet, Valérie, additional, Mourey, Lionel, additional, Daffé, Mamadou, additional, Lemassu, Anne, additional, André, Gwenaëlle, additional, and Marrakchi, Hedia, additional

Published
2022
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9. Additional file of Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality

Author

Vonick Sibut, Hennequet-Antier, Christelle, Bihan-Duval, Elisabeth Le, Marthey, Sylvain, Duclos, Michel J, and Berri, Cécile

Subjects
animal structures, food and beverages
Abstract

Additional file of Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality

Published
2020
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10. Additional file 3 of Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality

Author

Vonick Sibut, Hennequet-Antier, Christelle, Bihan-Duval, Elisabeth Le, Marthey, Sylvain, Duclos, Michel J, and Berri, Cécile

Subjects
animal structures, embryonic structures
Abstract

Additional file 3:List of the common genes that were differentially expressed in the two models (Fat vs. Lean chickens and G+ vs. G- chickens generated from the F2FL population). (DOC 34 KB)

Published
2020
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15. Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities

Author

Le Guillou, Sandrine, Leduc, Arlette, Laubier, Johann, Barbey, Sarah, Rossignol, Marie-Noëlle, Lefebvre, Rachel, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Domaine expérimental animal du Pin (SEA), and Institut National de la Recherche Agronomique (INRA)

Subjects
Epigenomics, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV]Life Sciences [q-bio], lcsh:R, Age Factors, lcsh:Medicine, food and beverages, Computational Biology, High-Throughput Nucleotide Sequencing, Breeding, Article, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, MicroRNAs, fluids and secretions, Milk, Species Specificity, Next-generation sequencing, Animals, lcsh:Q, Cattle, Gene expression, lcsh:Science, Transcriptome, Genetic Background
Abstract

International audience; The concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization of these components has been performed in several species, such as humans and bovine, depending on the stages of lactation. Here, we have studied the variation in milk microRNA composition according to genetic background. Using high throughput sequencing, we have characterized and compared the milk miRNomes of Holstein and Normande cattle, dairy breeds with distinct milk production features, in order to highlight microRNAs that are essential for regulation of the lactation process. In Holstein and Normande milk, 2,038 and 2,030 microRNAs were identified, respectively, with 1,771 common microRNAs, of which 1,049 were annotated and 722 were predicted. The comparison of the milk miRNomes of two breeds allowed to highlight 182 microRNAs displaying significant differences in the abundance. They are involved in the regulation of lipid metabolism and mammary morphogenesis and development, which affects lactation. Our results provide new insights into the regulation of molecular mechanisms involved in milk production.

Published
2019
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16. Influence of genetic background to the bovine milk microRNA composition

Author

Le Guillou, Sandrine, Laubier, Johann, Leduc, Antoine, Launay, Frédéric, Barbey, Sarah, Lefebvre, Rachel, Rossignol, Marie-Noëlle, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Domaine expérimental animal du Pin (SEA), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

17. Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities

Author

Leduc, Arlette, Laubier, Johann, Barbey, Sarah, Rossignol, Marie-Noelle, Lefebvre, Rachel, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, and Le Guillou, Sandrine

Subjects
composant du lait, fluids and secretions, origine génétique, variabilité génétique animale, micro arn, food and beverages, race holstein, race normande
Abstract

The concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization of these components has been performed in several species, such as humans and bovine, depending on the stages of lactation. Here, we have studied the variation in milk microRNA composition according to genetic background. Using high throughput sequencing, we have characterized and compared the milk miRNomes of Holstein and Normande cattle, dairy breeds with distinct milk production features, in order to highlight microRNAs that are essential for regulation of the lactation process. In Holstein and Normande milk, 2,038 and 2,030 microRNAs were identified, respectively, with 1,771 common microRNAs, of which 1,049 were annotated and 722 were predicted. The comparison of the milk miRNomes of two breeds allowed to highlight 182 microRNAs displaying significant differences in the abundance. They are involved in the regulation of lipid metabolism and mammary morphogenesis and development, which affects lactation. Our results provide new insights into the regulation of molecular mechanisms involved in milk production.

Published
2019

18. MOESM1 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Raphaelle Momal-Leisenring, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Marie-Hélène Pinard-Van Der Laan, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Abstract

Additional file 1 Additional file 1: Supplementary figures (S1-S26) and tables (S1-S15).

Published
2019
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19. A missense mutation in TYRP1 causes the chocolate plumage color in chicken and alters melanosome structure

Author

Li, Jingyi, Bed'hom, Bertrand, Marthey, Sylvain, Valade, Mathieu, Dureux, Audrey, Moroldo, Marco, Pechoux, Christine, Coville, Jean-Luc, Gourichon, David, Vieaud, Agathe, Dorshorst, Ben, Andersson, Leif, Tixier-Boichard, Michele, Li, Jingyi, Bed'hom, Bertrand, Marthey, Sylvain, Valade, Mathieu, Dureux, Audrey, Moroldo, Marco, Pechoux, Christine, Coville, Jean-Luc, Gourichon, David, Vieaud, Agathe, Dorshorst, Ben, Andersson, Leif, and Tixier-Boichard, Michele

Abstract

The chocolate plumage color in chickens is due to a sex-linked recessive mutation, choc, which dilutes eumelanin pigmentation. Because TYRP1 is sex-linked in chickens, and TYRP1 mutations determine brown coat color in mammals, TYRP1 appeared as the obvious candidate gene for the choc mutation. By combining gene mapping with gene capture, a complete association was identified between the chocolate phenotype and a missense mutation leading to a His214Asn change in the ZnA zinc-binding domain of the protein. A diagnostic test confirmed complete association by screening 428 non-chocolate chickens of various origins. This is the first TYRP1 mutation described in the chicken. Electron microscopy analysis showed that melanosomes were more numerous in feather follicles of chocolate chickens but exhibited an abnormal structure characterized by a granular content and an irregular shape. A similar altered morphology was observed on melanosomes of another TYRP1 mutant in birds, the roux mutation of the quail.

Published
2019
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21. Les microARNs de la glande mammaire et du lait. Convergence vers la définition d'une signature multi-espèces spécifique de la fonction de lactation

Author

Le Guillou, Sandrine, Mobuchon, Lenha, Marthey, Sylvain, Laloë, Denis, Bourdon, Céline, Boussaha, Mekki, Tosser, Gwenola, Gele, Marine, Boutinaud, Marion, Leroux, Christine, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Institut de l'élevage (IDELE), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, AgroParisTech-Institut National de la Recherche Agronomique (INRA), and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

National audience

Published
2018

22. The CRB-Anim web portal: access to biological resources for animal sciences

Author

Tixier-Boichard, Michele, Marthey, Sylvain, MARTHEY, Nicolas, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), and PIA CRB-Anim

Subjects
ressources génétiques, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], portail web, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

23. Bull sperm sncRNAs: A new source for potential fertility biomarkers?

Author

Sellem, Eli, Marthey, Sylvain, Kiefer, Hélène, Le Danvic, Chrystelle, Allais-Bonnet , Aurélie, Jouneau, Luc, Jammes, Hélène, Schibler, Laurent, Rau, Andrea, Allice, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), ANR SeQuamol - APIS- GENE, and British Society of Animal Science (BSAS). GBR.

Subjects
Reproductive Biology, sperme, Biologie du développement, Biologie de la reproduction, taureau, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Development Biology, biomarqueur, [SDV.BDD]Life Sciences [q-bio]/Development Biology, gestion de la fertilité, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

24. Influence des races bovines sur la composition en microARN du lait

Author

Le Guillou, Sandrine, Laubier, Johann, Leduc, Antoine, Gallard, Yves, Barbey, Sarah, Lefebvre, Rachel, Rossignol, Marie-Noelle, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Domaine expérimental animal du Pin (SEA), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

25. Milk microRNA composition depends on dairy cow breed

Author

Le Guillou, Sandrine, Laubier, Johann, Leduc, Antoine, Gallard, Yves, Barbey, Sarah, Lefebvre, Rachel, Krupova, Zuzana, Rossignol, Marie-Noelle, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Domaine expérimental animal du Pin (SEA), Institut National de la Recherche Agronomique (INRA), Excilone [Elancourt], and International Milk Genomics Consortium (IMGC).

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

26. Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kévin, Esquerre, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaëlle, Mompart, Florence, Quéré, Pascale, Robelin, David, San Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard - Van Der Laan, Marie-Helene, Klopp, Christophe, Tixier-Boichard, Michele, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Subjects
Functional annotation, Livestock, RNA-seq, ATAC-seq, Hi-C
Abstract

Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims at profiling the landscape of transcription (RNA-seq) and chromatin accessibility and conformation (ATAC-seq and Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species. RNA-seq assays allowed to considerably extend the available catalog of protein-coding and non-coding transcripts. Gene expression profiles were consistent with known metabolic/immune functions and revealed differentially expressed transcripts with unknown function, including new lncRNAs in syntenic regions. The majority of ATAC-seq peaks of chromatin accessibility mapped to putative regulatory regions, with an enrichment of predicted transcription factor binding sites in differentially accessible peaks. Hi-C provided the first set of genome-wide maps of three-dimensional interactions across livestock and showed consistency with results from gene expression and chromatin accessibility in topological compartments of the genomes. We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project. The global consistency between gene expression and chromatin structure data in these four livestock species adds up to previous findings in model animals. Overall, these results emphasize the value of FAANG for the research on domesticated animals and strengthen the importance of future meta-analyses of the reference datasets being generated by this community on different species.

Published
2018

27. Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality

Author

Marthey Sylvain, Le Bihan-Duval Elisabeth, Hennequet-Antier Christelle, Sibut Vonick, Duclos Michel J, and Berri Cécile

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The processing ability of poultry meat is highly related to its ultimate pH, the latter being mainly determined by the amount of glycogen in the muscle at death. The genetic determinism of glycogen and related meat quality traits has been established in the chicken but the molecular mechanisms involved in variations in these traits remain to be fully described. In this study, Chicken Genome Arrays (20 K) were used to compare muscle gene expression profiles of chickens from Fat (F) and Lean (L) lines that exhibited high and low muscle glycogen content, respectively, and of individuals exhibiting extremely high (G+) or low (G-) muscle glycogen content originating from the F2 cross between the Fat and Lean lines. Real-time RT-PCR was subsequently performed to validate the differential expression of genes either selected from the microarray analysis or whose function in regulating glycogen metabolism was well known. Results Among the genes found to be expressed in chicken P. major muscle, 197 and 254 transcripts appeared to be differentially expressed on microarrays for the F vs. L and the G+ vs. G- comparisons, respectively. Some involved particularly in lipid and carbohydrate metabolism were selected for further validation studies by real-time RT-PCR. We confirmed that, as in mammals, the down-regulation of CEBPB and RGS2 coincides with a decrease in peripheral adiposity in the chicken, but these genes are also suggested to affect muscle glycogen turnover through their role in the cAMP-dependent signalling pathway. Several other genes were suggested to have roles in the regulation of glycogen storage in chicken muscle. PDK4 may act as a glycogen sensor in muscle, UGDH may compete for glycogen synthesis by using UDP-glucose for glucoronidation, and PRKAB1, PRKAG2, and PHKD may impact on glycogen turnover in muscle, through AMP-activated signalling pathways. Conclusions This study is the first stage in the understanding of molecular mechanisms underlying variations in poultry meat quality. Large scale analyses are now required to validate the role of the genes identified and ultimately to find molecular markers that can be used for selection or to optimize rearing practices.

Published
2011
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28. FUNYBASE: a FUNgal phYlogenomic dataBASE

Author

Lopez-Villavicencio Manuela, Fournier Elisabeth, Giraud Tatiana, Gendrault Annie, Rodolphe François, Aguileta Gabriela, Marthey Sylvain, Gautier Angélique, Lebrun Marc-Henri, and Chiapello Hélène

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging. The aim of this study was to provide a reliable and integrated resource of orthologous gene families to perform comparative and phylogenetic analyses in fungi. Description FUNYBASE is a database dedicated to the analysis of fungal single-copy genes extracted from available fungal genomes sequences, their classification into reliable clusters of orthologs, and the assessment of their informative value for phylogenetic reconstruction based on amino acid sequences. The current release of FUNYBASE contains two types of protein data: (i) a complete set of protein sequences extracted from 30 public fungal genomes and classified into clusters of orthologs using a robust automated procedure, and (ii) a subset of 246 reliable ortholog clusters present as single copy genes in 21 fungal genomes. For each of these 246 ortholog clusters, phylogenetic trees were reconstructed based on their amino acid sequences. To assess the informative value of each ortholog cluster, each was compared to a reference species tree constructed using a concatenation of roughly half of the 246 sequences that are best approximated by the WAG evolutionary model. The orthologs were classified according to a topological score, which measures their ability to recover the same topology as the reference species tree. The full results of these analyses are available on-line with a user-friendly interface that allows for searches to be performed by species name, the ortholog cluster, various keywords, or using the BLAST algorithm. Examples of fruitful utilization of FUNYBASE for investigation of fungal phylogenetics are also presented. Conclusion FUNYBASE constitutes a novel and useful resource for two types of analyses: (i) comparative studies can be greatly facilitated by reliable clusters of orthologs across sets of user-defined fungal genomes, and (ii) phylogenetic reconstruction can be improved by identifying genes with the highest informative value at the desired taxonomic level.

Published
2008
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29. Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes

Author

Devier Benjamin, Rodolphe François, Hood Michael E, Gendrault Annie, Chiapello Hélène, Marthey Sylvain, Yockteng Roxana, Wincker Patrick, Dossat Carole, and Giraud Tatiana

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The basidiomycete fungus Microbotryum violaceum is responsible for the anther-smut disease in many plants of the Caryophyllaceae family and is a model in genetics and evolutionary biology. Infection is initiated by dikaryotic hyphae produced after the conjugation of two haploid sporidia of opposite mating type. This study describes M. violaceum ESTs corresponding to nuclear genes expressed during conjugation and early hyphal production. Results A normalized cDNA library generated 24,128 sequences, which were assembled into 7,765 unique genes; 25.2% of them displayed significant similarity to annotated proteins from other organisms, 74.3% a weak similarity to the same set of known proteins, and 0.5% were orphans. We identified putative pheromone receptors and genes that in other fungi are involved in the mating process. We also identified many sequences similar to genes known to be involved in pathogenicity in other fungi. The M. violaceum EST database, MICROBASE, is available on the Web and provides access to the sequences, assembled contigs, annotations and programs to compare similarities against MICROBASE. Conclusion This study provides a basis for cloning the mating type locus, for further investigation of pathogenicity genes in the anther smut fungi, and for comparative genomics.

Published
2007
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30. Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]

Author

Foissac, Sylvain, Djebali Quelen, Sarah, ACLOQUE, Hervé, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Derrien, Thomas, Drouet, Françoise, Esquerre, Diane, Fabre, Stéphane, Gaspin, Christine, GONZALEZ, Ignacio, Goubil, Adeline, Klopp, Christophe, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Mompart, Florence, Munyard, Kylie, Muret, Kévin, Pollet, Sophie, Quéré, Pascale, Rau, Andrea, Robelin, David, San Cristobal, Magali, Tixier-Boichard, Michele, Tosser-Klopp, Gwenola, Villa-Vialaneix, Nathalie, Vincent-Naulleau, Silvia, Zytnicki, Matthias, Pinard - Van Der Laan, Marie-Helene, Lagarrigue, Sandrine, Giuffra, Elisabetta, Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), 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], Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), Institut National de la Recherche Agronomique (INRA), Dynamiques Forestières dans l'Espace Rural (DYNAFOR), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-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), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), FR-AgENCODE, Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), 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), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
multispecies, Hi-C, [SDV]Life Sciences [q-bio], Multispecies, Biologie animale, Functional annotation of animal genome (FAANG), functional annotation of animal genome (FAANG), ATAC-seq, RNA-seq
Abstract

Functional annotation of livestock genomes is a critical and obvious next step to derive maximum benefit for agriculture, animal science, animal welfare and human health. The aim of the Fr-AgENCODE project is to generate multi-species functional genome annotations by applying high-throughput molecular assays on three target tissues/cells relevant to the study of immune and metabolic traits. An extensive collection of stored samples from other tissues is available for further use (FAANG Biosamples ‘FR-AGENCODE’). From each of two males and two females per species (pig, cattle, goat, chicken), strand-oriented RNA-seq and chromatin accessibility ATAC-seq assays were performed on liver tissue and on two T-cell types (CD3+CD4+&CD3+CD8+) sorted from blood (mammals) or spleen (chicken). Chromosome Conformation Capture (in situ Hi-C) was also carried out on liver. Sequencing reads from the 3 assays were processed using standard processing pipelines. While most (50–70%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts and genes were found, including extensions of annotated protein-coding genes and new lncRNAs (see abstract #69857). Consistency of ATAC-seq results was confirmed by the significant proportion of called peaks in promoter regions (36–66%) and by the specific accumulation pattern of peaks around gene starts (TSS) v. gene ends (TTS). Principal Component Analyses for RNA-seq (based on quantified gene expression) and ATAC-seq (based on quantified chromatin accessibility) highlighted clusters characterised by cell type and sex in all species. From Hi-C data, we generated 40kb-resolution interaction maps, profiled a genome-wide Directionality Index and identified from 4,100 (chicken) to 12,100 (pig) topologically-associating do- mains (TADs). Correlations were reported between RNA-seq and ATAC-seq results (see abstract #71581). In summary, we present here an overview of the first multi-species and -tissue annotations of chromatin accessibility and genome architecture related to gene expression for farm animals.

Published
2017

31. Sunflower oil supplementation affects the expression of miR-20a-5p and miR-142-5p in the lactating bovine mammary gland

Author

Mobuchon, Lenha, Le Guillou, Sandrine, Marthey, Sylvain, Laubier, Johann, Laloë, Denis, Bes, Sébastien, Le Provost, Fabienne, Leroux, Christine, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, INRA, ApisGene under the NutriMirMa project, AIP BioRessources, VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
bovin, Physiology, [SDV]Life Sciences [q-bio], lcsh:Medicine, Biochemistry, [SHS]Humanities and Social Sciences, Plant Products, Medicine and Health Sciences, Sunflower Oil, lcsh:Science, Flowering Plants, Reverse Transcriptase Polymerase Chain Reaction, Eukaryota, Agriculture, Plants, Mammary Glands, Lipids, Body Fluids, Nucleic acids, Sunflower, Milk, Female, Anatomy, expression des gènes, Research Article, Real-Time Polymerase Chain Reaction, Vegetable Oils, huile de tournesol, Beverages, Mammary Glands, Animal, Exocrine Glands, Genetics, Animals, Lactation, [INFO]Computer Science [cs], Non-coding RNA, Nutrition, [SDV.GEN]Life Sciences [q-bio]/Genetics, Biology and life sciences, lcsh:R, Reproductive System, Organisms, Lipid Metabolism, Agronomy, Gene regulation, Diet, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, MicroRNAs, Metabolism, glande mammaire, RNA, lcsh:Q, Cattle, Gene expression, Breast Tissue, Crop Science
Abstract

International audience; Oil supplementation in dairy cattle diets is used to modulate milk fat composition, as well as the expression of mammary lipogenic genes, whose regulation remains unclear. MiRNAs are small non-coding RNA considered as crucial regulators of gene expression, offering clues to explain the mechanism underlying gene nutriregulation. The present study was designed to identify miRNAs whose expression in the cow mammary gland is modulated by sunflower oil supplementation. MiRNomes were obtained using RNAseq technology from the mammary gland of lactating cows receiving a low forage diet, supplemented or not with 4% sunflower oil. Among the 272 miRNAs characterized, eight were selected for RT-qPCR validations, showing the significant down-regulation of miR-142-5p and miR-20a-5p by sunflower supplementation. These two miRNAs are predicted to target genes whose expression was reported as differentially expressed by sunflower supplementation. Among their putative targets, ELOVL6 gene involved in lipid metabolism has been studied. However, a first analysis did not show its significant down-regulation, in response to the over-expression of miR-142-5p, of miR-20a-5p, or both, in a bovine mammary epithelial cell line. However, a clearer understanding of the miRNA expression by lipid supplementation would help to decipher the regulation of lactating cow mammary gland in response to nutrition.

Published
2017
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33. Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and One Roe Deer Collected in Europe

Author

Dugat, Thibaud, primary, Rossignol, Marie-Noëlle, additional, Rué, Olivier, additional, Loux, Valentin, additional, Marthey, Sylvain, additional, Moroldo, Marco, additional, Silaghi, Cornelia, additional, Höper, Dirk, additional, Fröhlich, Julia, additional, Pfeffer, Martin, additional, Zweygarth, Erich, additional, Lagrée, Anne-Claire, additional, Boulouis, Henri-Jean, additional, and Haddad, Nadia, additional

Published
2016
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34. Using NGS data to characterize genetics of meet-type and egg-type chicken lines

Author

Roux, Pierre-François, Lecerf, Frédéric, Djari, Anis, Esquerre, Diane, Marthey, Sylvain, Zerjal, Tatiana, Le Bihan-Duval, Elisabeth, Klopp, Christophe, Moroldo, Marco, Estelle, Jordi, Désert, Colette, Bed'Hom, Bertrand, Tixier Boichard, Michèle, Demeure, Olivier, Lagarrigue, Sandrine, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Unité de Biométrie et Intelligence Artificielle (UBIA), 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, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Recherches Avicoles (URA), Génétique Physiologie et Systèmes d'Elevage, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, analyse de génome, adiposité, sélection génétique, caractérisation génomique, poulet, efficience alimentaire
Abstract

Session 25. Free communications - molecular genetics; absent

Published
2013

35. Identification of candidate polymorphism in a QTL region by combining eQTL mapping with NGS data

Author

Roux, Pierre-François, Blum, Yuna, Désert, Colette, Djari, Anis, Esquerre, Diane, Le Bihan-Duval, Elisabeth, Bed'Hom, Bertrand, Le Roy, Pascale, Lecerf, Frédéric, Moroldo, Marco, Marthey, Sylvain, Klopp, Christophe, Lagarrigue, Sandrine, Demeure, Olivier, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Unité de Biométrie et Intelligence Artificielle (UBIA), 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, Unité de Recherches Avicoles (URA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage, Recherches Avicoles (SRA), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, cartographie de qtl, adiposité, poulet, approche génomique
Abstract

Session 25. Free communications - molecular genetics; absent

Published
2013

37. PrP and Shadoo are required for trophoblastic development

Author

Passet, Bruno, YOUNG, Rachel, Vilotte, Jean Luc, Makhzami, Samira, Jaffrezic, Florence, Halliez, Sophie, Bouet, Stephan, Marthey, Sylvain, Khalife, Manal, Kanellopoulos-Langevin, Colette, Beringue, Vincent, Le Provost, Fabienne, Laude, Hubert, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), and ProdInra, Archive Ouverte

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract

absent

Published
2012

38. Efficiency of heterologous capture for targeted resequencing of the Major Histocompatibility Complex in Suidae and Tayassuidae

Author

Gongora, Jaime, Mach, Nuria, Estelle, Jordi, Wahlberg, Per, Marthey, Sylvain, Lecardonnel, Jerôme, Bihoreau, Marie-Thérèse, Gaillard, Claire, Moroldo, Marco, Faculty of Veterinary Medicine, The University of Sydney, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Labo/service de l'auteur, Ville service, Pays service.

Subjects
genomic, MHC (Major Histocompatibility Complex), [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Suidae, Tayassuidae
Abstract

Sequence capture is a widespread and cost effective approach to resequence specific genomic regions on large sets of individuals. To date, this approach has mainly been used to target orthologous loci within the same species ('homologous' capture). Our aim was to test the efficiency of this method across closely or distantly related species ('heterologous' capture). Specifically, we focused on the MHC locus, which is one of the most dynamic regions of mammalian genomes, and a model to study host-pathogen coevolution. A 385K solid phase array (NimbleGen) encompassing the MHC was designed using the Sus scrofa Hp1a.0 haplotype as a reference (http://vega.sanger.ac.uk/index.html). Individuals from 9 species of Suidae (n=69) and 2 species of Tayassuidae (n=19) were selected for the study. Sets of 12 uniquely indexed sequencing libraries were prepared using Illumina kits, pooled, enriched, and sequenced on a HiSeq platform. In Suidae, the average values of coverage and specificity (% on target sequences) were respectively 86x and 32%. Results varied significantly across libraries, e.g. decreasing the number of cycles during PCR steps reduced the percentage of duplicate reads, but without improving specificity. On the other hand, in Tayassuidae both the coverage and the specificity showed lower efficiency. We can conclude that heterologous capture is a reliable technique at the level of Suidae, while in the case of Tayassuidae further optimization will be required to achieve better results. Other analyses are ongoing to test if this method could be suitable to study structural variation.

Published
2012

39. Novel models and strategies to unravel the genetic pathways involved in horn ontogenesis

Author

Capitan, Aurelien, Grohs, Cecile, Bonnet, Agnes, Pinton, Alain, Leguienne, Brigitte, Le Bourhis, Daniel, Bouchez, Olivier, Klopp, Christophe, Bouet, Stephan, Wahlberg, Per, Marthey, Sylvain, Richard, Christophe, Chantry-Darmon, Céline, Gallard, Yves, Pailhoux, Eric, Rocha, Dominique, Boichard, Didier, Eggen, Andre, Genetics Team, Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, 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), Research and Development Team, Unité de Biométrie et Intelligence Artificielle (UBIA), Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Domaine expérimental animal du Pin (SEA), Apisgene Hornout, Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), 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
corne, bovin, [SDV]Life Sciences [q-bio], cornes
Abstract

Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access; absent

Published
2012

40. Gènes différentiellement exprimés dans le tissu adipeux de vaches laitières portant des haplotypes contrastés pour un QTL de fertilité femelle du chromosome 3

Author

Coyral-Castel, Stéphanie, Rame, Christelle, Elis, Sébastien, Cognie, Juliette, Fritz, S., Lecardonnel, Jérôme, Hennequet-Antier, Christelle, Marthey, Sylvain, Esquerre, Diane, Dupont, Joëlle, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Unité de Recherches Avicoles (URA), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)

Subjects
bovin, bovin laitier, expression génique, GENETIQUE ANIMALE, qtl, vache laitière, [SDV]Life Sciences [q-bio], reproduction animale, fertilité animale, tissu adipeux, chromosome, chromosome 3
Abstract

absent

Published
2010

42. Hybridization-based targeted enrichment and second generation sequencing applied to domestic animals

Author

Wahlberg, Per, Capitan, Aurelien, Bihoreau, Marie-Therese, Rodriguez, Sabrina, Grohs, Cecile, Marthey, Sylvain, Esquerre, Diane, Gut, Marta, Bed'Hom, Bertrand, Bourneuf, Emmanuelle, Gut, Ivo, Rogel Gaillard, Claire, Hugot, Karine, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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, DSV/iRCM/SREIT/LREG, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)-Université de Toulouse (UT)

Subjects
animal domestique, phénotype, [SDV]Life Sciences [q-bio], mutation, hybridation, ComputingMilieux_MISCELLANEOUS, génomique comparée
Abstract

International audience

Published
2010

44. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC

Author

Jaratlerdsiri, Weerachai, Deakin, Janine, Godinez, Ricardo M., Shan, Xueyan, Peterson, Daniel G., Marthey, Sylvain, Lyons, Eric, McCarthy, Fiona M., Isberg, Sally R., Higgins, Damien P., Chong, Amanda Y., John, John St, Glenn, Travis C., Ray, David A., Gongora, Jaime, Jaratlerdsiri, Weerachai, Deakin, Janine, Godinez, Ricardo M., Shan, Xueyan, Peterson, Daniel G., Marthey, Sylvain, Lyons, Eric, McCarthy, Fiona M., Isberg, Sally R., Higgins, Damien P., Chong, Amanda Y., John, John St, Glenn, Travis C., Ray, David A., and Gongora, Jaime

Abstract

The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

Published
2014

45. Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC

Author

Jaratlerdsiri, Weerachai, primary, Deakin, Janine, additional, Godinez, Ricardo M., additional, Shan, Xueyan, additional, Peterson, Daniel G., additional, Marthey, Sylvain, additional, Lyons, Eric, additional, McCarthy, Fiona M., additional, Isberg, Sally R., additional, Higgins, Damien P., additional, Chong, Amanda Y., additional, John, John St, additional, Glenn, Travis C., additional, Ray, David A., additional, and Gongora, Jaime, additional

Published
2014
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48. Prion Protein and Shadoo Are Involved in Overlapping Embryonic Pathways and Trophoblastic Development

Author

Passet, Bruno, primary, Young, Rachel, additional, Makhzami, Samira, additional, Vilotte, Marthe, additional, Jaffrezic, Florence, additional, Halliez, Sophie, additional, Bouet, Stéphan, additional, Marthey, Sylvain, additional, Khalifé, Manal, additional, Kanellopoulos-Langevin, Colette, additional, Béringue, Vincent, additional, Le Provost, Fabienne, additional, Laude, Hubert, additional, and Vilotte, Jean-Luc, additional

Published
2012
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49. Transcriptomic Analysis Brings New Insight into the Biological Role of the Prion Protein during Mouse Embryogenesis

Author

Khalifé, Manal, primary, Young, Rachel, additional, Passet, Bruno, additional, Halliez, Sophie, additional, Vilotte, Marthe, additional, Jaffrezic, Florence, additional, Marthey, Sylvain, additional, Béringue, Vincent, additional, Vaiman, Daniel, additional, Le Provost, Fabienne, additional, Laude, Hubert, additional, and Vilotte, Jean-Luc, additional

Published
2011
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50. FUNYBASE: a FUNgal phYlogenomic dataBASE

Author

Marthey, Sylvain, primary, Aguileta, Gabriela, additional, Rodolphe, François, additional, Gendrault, Annie, additional, Giraud, Tatiana, additional, Fournier, Elisabeth, additional, Lopez-Villavicencio, Manuela, additional, Gautier, Angélique, additional, Lebrun, Marc-Henri, additional, and Chiapello, Hélène, additional

Published
2008
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