title: Identification of the mammalian Not gene via a phylogenomic approach.
abstract: Despite the great morphological diversity of early embryos, the underlying mechanisms of gastrulation are known to be broadly conserved in vertebrates. However, a number of genes characterized as fulfilling an essential function in this process in several model organisms display no clear ortholog in mammalian genomes. We have devised an in silico phylogenomic approach, based on exhaustive similarity searches in vertebrate genomes and subsequent bayesian phylogenetic analyses, to identify such missing genes, presumed to be highly divergent. This approach has been used to identify mammalian orthologs of Not, an homeodomain containing gene previously characterized in Xenopus, chick and zebrafish as playing a critical role in the formation of the notochord. This attempt led to the identification of a highly divergent mammalian Not-related gene in the mouse, human and rat. The results from phylogenetic reconstructions, synteny analyses, expression pattern analyses in wild-type and mutant mouse embryos, and overexpression experiments in Xenopus embryos converge to confirm these genes as representatives of the Not family in mammals. The identification of the mammalian Not gene delivers an important component for the understanding of the genetics underlying notochord formation in mammals and its evolution among vertebrates. The phylogenomic method used to retrieve this gene thus provides a tool, which can complement or validate genome annotations in situations when they are weakly supported.
authors.affiliation: Développement et Evolution des Vertébrés, UMR 8080, Université Paris-Sud, 91405 ORSAY, France.
authors.forename: J-L
authors.initials: JL
authors.lastname: Plouhinec
authors.forename: C
authors.initials: C
authors.lastname: Granier
authors.forename: C
authors.initials: C
authors.lastname: Le Mentec
authors.forename: K A
authors.initials: KA
authors.lastname: Lawson
authors.forename: D
authors.initials: D
authors.lastname: Sabéran-Djoneidi
authors.forename: J
authors.initials: J
authors.lastname: Aghion
authors.forename: D L
authors.initials: DL
authors.lastname: Shi
authors.forename: J
authors.initials: J
authors.lastname: Collignon
authors.forename: S
authors.initials: S
authors.lastname: Mazan
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001499:Bayes Theorem; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family; D057126:Nuclear Receptor Subfamily 4, Group A, Member 2; D010802:Phylogeny; D017433:Protein Structure, Secondary; D051381:Rats; D026801:Synteny; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014981:Xenopus
chemical_list: D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; C539882:NR4A2 protein, human; C489656:Not protein, mouse; C539883:Nr4a2 protein, mouse; C539884:Nr4a2 protein, rat; D057126:Nuclear Receptor Subfamily 4, Group A, Member 2; D014157:Transcription Factors