Phylogenetic analysis and positive-selection site detecting of vascular endothelial growth factor family in vertebrates

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• 作者：Wenwu He ; Yanyan Tang ; Bin Qi ; Chuansen Lu ; Chao Qin ; Yunfei Wei ; Jiachao Yi ; Mingwu Chen
• 关键词：VEGF ; vascular endothelial growth factor ; NCBI ; National Center for Biotechnology Information ; PGF ; placenta growth factor ; GTR ; general time reversible ; GTR  ; +  ; G  ; +  ; I ; general time reversible plus gamma distribution plus invariant sites model ; MCMC ; Markov Chain Monte Carlo ; LRT ; likelihood ratio test ; NEB ; naive empirical Bayes ; BEB ; Bayes empirical Bayes ; PDGF ; platelet-derived growth factor ; PPs ; posterior probabilities ; Nrp-1 ; neuropilin-1 ; 蠅 ; nucleotide substitution rate
• 刊名：Gene
• 出版年：10 February, 2014
• 年：2014
• 卷：535
• 期：2
• 页码：345-352
• 全文大小：1027 K

文摘

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.