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BMC Genomics

, 18:534

Prokaryote microbial genomics

Abstract

BackgroundCanine parvovirus CPV type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar to some RNA viruses. Therefore, it is important to trace the evolution of CPV to monitor the appearance of mutations that might affect vaccine effectiveness.

ResultsOur analysis shows that the VP2 genes of CPV isolated from 1979 to 2016 are divided into six groups: GI, GII, GIII, GIV, GV, and GVI. Amino acid mutation analysis revealed several undiscovered important mutation sites: F267Y, Y324I, and T440A. Of note, the evolutionary rate of the CPV VP2 gene from Asia and Europe decreased. Codon usage analysis showed that the VP2 gene of CPV exhibits high bias with an ENC ranging from 34.93 to 36.7. Furthermore, we demonstrate that natural selection plays a major role compared to mutation pressure driving CPV evolution.

ConclusionsThere are few studies on the codon usage of CPV. Here, we comprehensively studied the genetic evolution, codon usage pattern, and evolutionary characterization of the VP2 gene of CPV. The novel findings revealing the evolutionary process of CPV will greatly serve future CPV research.

KeywordsCanine parvovirus type 2 VP2 Phylogenetic analysis Evolution Codon usage AbbreviationsCOACorrespondence analysis

CPV-2Canine parvovirus type 2

ENCEffective number of codons

PCAPrincipal component analysis

RSCUThe relative synonymous codon usage

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-017-3935-8 contains supplementary material, which is available to authorized users.

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Autor: Gairu Li - Senlin Ji - Xiaofeng Zhai - Yuxiang Zhang - Jie Liu - Mengyan Zhu - Jiyong Zhou - Shuo Su

Fuente: https://link.springer.com/



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