Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus

Hai-Feng Tian; Qiao-Mu Hu; Han-Bing Xiao; Ling-Bing Zeng; Yan Meng; Zhong Li

doi:10.1016/j.meegid.2020.104379

Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus

Infect Genet Evol. 2020 Oct:84:104379. doi: 10.1016/j.meegid.2020.104379. Epub 2020 Jun 1.

Authors

Hai-Feng Tian¹, Qiao-Mu Hu¹, Han-Bing Xiao¹, Ling-Bing Zeng¹, Yan Meng², Zhong Li³

Affiliations

¹ Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
² Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China. Electronic address: mengy@yfi.ac.cn.
³ Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China. Electronic address: lizhong@yfi.ac.cn.

PMID: 32497680
DOI: 10.1016/j.meegid.2020.104379

Abstract

The Ranavirus (one genus of Iridovidae family) is an emerging pathogen that infects fish, amphibian, and reptiles, and causes great economical loss and ecological threat to farmed and wild animals globally. The major capsid protein (MCP) has been used as genetic typing marker and as target to design vaccines. Herein, the codon usage pattern of 73 MCP genes of Ranavirus and Lymphocystivirus are studied by calculating effective number of codons (ENC), relative synonymous codon usage (RSCU), codon adaptation index (CAI), and relative codon deoptimization index (RCDI), and similarity index (SiD). The Ranavirus are confirmed to be classified into five groups by using phylogenetic analysis, and varied nucleotide compositions and hierarchical cluster analysis based on RSCU. The results revealed different codon usage patterns among Lymphocystivirus and five groups of Ranavirus. Ranavirus had six over-represented codons ended with G/C nucleotide, while Lymphocystivirus had six over-represented codons ended with A/T nucleotide. A comparative analysis of parameters that define virus and host relatedness in terms of codon usage were analyzed indicated that Amphibian-like ranaviruses (ALRVs) seem to possess lower ENC values and higher CAIs in contrast to other ranaviruses isolated from fishes, and two groups (FV3-like and CMTV-like group) of them had received higher selection pressure from their hosts as having higher relative codon deoptimization index (RCDI) and similarity index (SiD). The correspondence analysis (COA) and Spearman's rank correlation analyses revealed that nucleotide compositions, relative dinucleotide frequency, mutation pressure, and natural translational selection shape the codon usage pattern in MCP genes and the ENC-GC_3S and neutrality plots indicated that the natural selection is the predominant factor. These results contribute to understanding the evolution of Ranavirus and their adaptions to their hosts.

Keywords: Codon usage bias; MCP; Mutation pressure; Natural selection; Nucleotide composition; Ranavirus.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Capsid Proteins / genetics
Capsid Proteins / metabolism*
Codon Usage
Evolution, Molecular
Gene Expression Regulation, Viral / physiology*
Iridoviridae / genetics
Iridoviridae / metabolism*
Phylogeny
Ranavirus / genetics
Ranavirus / metabolism*

Substances

Capsid Proteins
major capsid protein, Iridovirus