title: Phylogenetic analysis and positive-selection site detecting of vascular endothelial growth factor family in vertebrates.
abstract: Vascular endothelial growth factor (VEGF), known to play an important role in vascular homeostasis, vascular integrity and angiogenesis, is little known about the evolutionary relationship of its five members especially the role of gene duplication and natural selection in the evolution of the VEGF family. In this study, seventy-five full-length cDNA sequences from 33 vertebrate species were extracted from the NCBI's GenBank, UniProt protein database and the Ensembl database. By phylogenetic analyses, we investigated the origin, conservation, and evolution of the VEGFs. Five VEGF family members in vertebrates might be formed by gene duplication. The inferred evolutionary transitions that separate members which belong to different gene clusters correlated with changes in functional properties. Selection analysis and protein structure analysis were combined to explain the relationship of the site-specific evolution in the vertebrate VEGF family. Eleven positive selection sites, one transmembrane region and the active sites were detected in this process.
authors.affiliation: Department of Cardiothoracic Surgery, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China; Department of Cardiothoracic Surgery, Nanchong Central Hospital, The Second Clinical College of North Sichuan Medical college, Nanchong, Sichuan, PR China.
authors.forename: Wenwu
authors.initials: W
authors.lastname: He
authors.affiliation: Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China.
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Qi
authors.affiliation: Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China.
authors.forename: Chuansen
authors.initials: C
authors.lastname: Lu
authors.affiliation: Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Qin
authors.affiliation: Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China.
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Wei
authors.affiliation: Department of Neurology, Liugang Hospital, Liuzhou, Guangxi, China.
authors.forename: Jiachao
authors.initials: J
authors.lastname: Yi
authors.affiliation: Department of Cardiothoracic Surgery, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China. Electronic address: chen535@126.com.
authors.forename: Mingwu
authors.initials: M
authors.lastname: Chen
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030541:Databases, Genetic; D019143:Evolution, Molecular; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D011487:Protein Conformation; D012641:Selection, Genetic; D016415:Sequence Alignment; D042461:Vascular Endothelial Growth Factor A / Q000737:chemistry / Q000235:genetics*; D014714:Vertebrates / Q000145:classification / Q000235:genetics*
chemical_list: D042461:Vascular Endothelial Growth Factor A
keywords: ANOFI; Anoplopoma fimbria; BEB; BOVIN; Bayes empirical Bayes; Biological evolution; Bos taurus; CALJA; CAPHI; CAVPO; CHICK; COTCO; COTJA; Callithrix jacchus; Canis familiaris; Capra hircus; Cavia porcellus; Coturnix coturnix; Coturnix coturnix japonica; DANRE; DOG; Danio rerio; Equus caballus; FECA; Felis catus; GTR; GTR+G+I; Gallus gallus; HORSE; HUMAN; Homo sapiens; LRT; M0; M1a; M2a; M3; M7; M8; MACMU; MCMC; MESAU; MONDO; MOUSE; Macaca mulatta; Markov Chain Monte Carlo; Mesocricetus auratus; Monodelphis domestica; Mus musculus; NANEH; NCBI; NEB; Nannospalax ehrenbergi; National Center for Biotechnology Information; Natural selection; Nrp-1; ONCMY; ORNAN; OSMO; Oncorhynchus mykiss; Ornithorhynchus anatinus; Oryctolagus cuniculus; Osmerus mordax; Ovis aries; PANHO; PDGF; PGF; PIG; PPs; PSEGE; PSEUDO; Pantholops hodgsonii; Pseudochaenichthys georgianus; Pseudocowpox virus; RABIT; RAT; Rattus norvegicus; SALSA; SHEEP; Salmo salar; Sus scrofa; VEGF; Vascular endothelial growth factor (VEGF); Vertebrates; XENLA; XENTR; Xenopus laevis; Xenopus tropicalis; beta & ω model; beta model; dN; dS; discrete model; general time reversible; general time reversible plus gamma distribution plus invariant sites model; likelihood ratio test; naive empirical Bayes; nearly neutral model; neuropilin-1; nonsynonymous; nucleotide substitution rate ratio; one ratio model; placenta growth factor; platelet-derived growth factor; positive selection model; posterior probabilities; synonymous; vascular endothelial growth factor; ω