title: The loss of adipokine genes in the chicken genome and implications for insulin metabolism.
abstract: Gene loss is one of the main drivers in the evolution of genomes and species. The demonstration that a gene has been lost by pseudogenization is truly complete when one finds the pseudogene in the orthologous genomic region with respect to active genes in other species. In some cases, the identification of such orthologous loci is not possible because of chromosomal rearrangements or if the gene of interest has not yet been sequenced. This question is particularly important in the case of birds because the genomes of avian species possess only about 15,000 predicted genes, in comparison with 20,000 in mammals. Yet, gene loss raises the question of which functions are affected by the changes in gene counts. We describe a systematic approach that makes it possible to demonstrate gene loss in the chicken genome even if a pseudogene has not been found. By using phylogenetic and synteny analysis in vertebrates, genome-wide comparisons between the chicken genome and expressed sequence tags, RNAseq data analysis, statistical analysis of the chicken genome, and radiation hybrid mapping, we show that resistin, TNFα, and PAI-1 (SERPINE1), three genes encoding adipokines inhibiting insulin sensitivity, have been lost in chicken and zebra finch genomes. Moreover, omentin, a gene encoding an adipokine that enhances insulin sensitivity, has also been lost in the chicken genome. Overall, only one adipokine inhibiting insulin sensitivity and five adipokines enhancing insulin sensitivity are still present in the chicken genome. These genetic differences between mammals and chicken, given the functions of the genes in mammals, would have dramatic consequences on chicken endocrinology, leading to novel equilibriums especially in the regulation of energy metabolism, insulin sensitivity, as well as appetite and reproduction.
authors.affiliation: UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France UMR7247, CNRS, Nouzilly, France Université François Rabelais de Tours, Tours, France Institut Français du Cheval et de l'Equitation, Nouzilly, France.
authors.forename: Nataša
authors.initials: N
authors.lastname: Daković
authors.affiliation: UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France UMR7247, CNRS, Nouzilly, France Université François Rabelais de Tours, Tours, France Institut Français du Cheval et de l'Equitation, Nouzilly, France.
authors.forename: Morgane
authors.initials: M
authors.lastname: Térézol
authors.affiliation: UMR1388 INRA/INPT ENSAT/INPT ENVT, Génétique, Physiologie et Systèmes d'élevage, INRA, Castanet Tolosan, France.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Pitel
authors.affiliation: UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France UMR7247, CNRS, Nouzilly, France Université François Rabelais de Tours, Tours, France Institut Français du Cheval et de l'Equitation, Nouzilly, France.
authors.forename: Virginie
authors.initials: V
authors.lastname: Maillard
authors.affiliation: UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France UMR7247, CNRS, Nouzilly, France Université François Rabelais de Tours, Tours, France Institut Français du Cheval et de l'Equitation, Nouzilly, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Elis
authors.affiliation: UMR1388 INRA/INPT ENSAT/INPT ENVT, Génétique, Physiologie et Systèmes d'élevage, INRA, Castanet Tolosan, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Leroux
authors.affiliation: INRA, Agrocampus - Ouest, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'élevage, Saint-Gilles.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Lagarrigue
authors.affiliation: INRA, Agrocampus - Ouest, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'élevage, Saint-Gilles.
authors.forename: Florence
authors.initials: F
authors.lastname: Gondret
authors.affiliation: INRA, SIGENAE, Toulouse, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Baeza
authors.affiliation: UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France.
authors.forename: Michel J
authors.initials: MJ
authors.lastname: Duclos
authors.affiliation: INRA, UR83, Recherches Avicoles, Nouzilly, France UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France.
authors.forename: Hugues
authors.initials: H
authors.lastname: Roest Crollius
authors.affiliation: UMR85 Physiologie de la Reproduction et des Comportements, INRA, Nouzilly, France UMR7247, CNRS, Nouzilly, France Université François Rabelais de Tours, Tours, France Institut Français du Cheval et de l'Equitation, Nouzilly, France Philippe.Monget@tours.inra.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Monget
mesh_terms: D054392:Adipokines / Q000235:genetics*; D000818:Animals; D030161:Avian Proteins / Q000235:genetics*; D002645:Chickens / Q000235:genetics*; D019143:Evolution, Molecular; D005260:Female; D017353:Gene Deletion; D007328:Insulin / Q000378:metabolism*; D008297:Male; D010802:Phylogeny; D012098:Reproduction / Q000235:genetics; D017423:Sequence Analysis, RNA; D026801:Synteny; D014714:Vertebrates / Q000235:genetics
chemical_list: D054392:Adipokines; D030161:Avian Proteins; D007328:Insulin
keywords: adipokines; chicken; insulin resistance