Abstract
Two species of the DNA virus Torque teno sus virus (TTSuV), TTSuV1 and TTSuV2, have become widely distributed in pig-farming countries in recent years. In this study, we performed a comprehensive analysis of synonymous codon usage bias in 41 available TTSuV2 coding sequences (CDS), and compared the codon usage patterns of TTSuV2 and TTSuV1. TTSuV codon usage patterns were found to be phylogenetically conserved. Values for the effective number of codons (ENC) indicated that the overall extent of codon usage bias in both TTSuV2 and TTSuV1 was not significant, the most frequently occurring codons had an A or C at the third codon position. Correspondence analysis (COA) was performed and TTSuV2 and TTSuV1 sequences were located in different quadrants of the first two major axes. A plot of the ENC revealed that compositional constraint was the major factor determining the codon usage bias for TTSuV2. In addition, hierarchical cluster analysis of 41 TTSuV2 isolates based on relative synonymous codon usage (RSCU) values suggested that there was no association between geographic distribution and codon bias of TTSuV2 sequences. Finally, the comparison of RSCU for TTSuV2, TTSuV1 and the corresponding host sequence indicated that the codon usage pattern of TTSuV2 was similar to that of TTSuV1. However the similarity was low for each virus and its host. These conclusions provide important insight into the synonymous codon usage pattern of TTSuV2, as well as better understangding of the molecular evolution of TTSuV2 genomes.
Highlights
It is well known that the 64 codons of the genetic code encode the 20 standard amino acids as well as three translation termination signals (UAA, UAG, UGA)
It was necessary to exclude any TTSuV2 and Torque teno sus virus 1 (TTSuV1) sequences found to be recombinant from further analysis
The resulting graph provided no evidence for recombination within or between TTSuV2 and TTSuV1 sequences
Summary
It is well known that the 64 codons of the genetic code encode the 20 standard amino acids as well as three translation termination signals (UAA, UAG, UGA). Codons encoding the same amino acid are referred to as synonymous codons. Studies have indicated that synonymous codon usage is non-random and species-specific [1]. Some synonymous codons are more frequent than others both within and between genes, and this phenomenon is termed synonymous codon usage bias [2]. Codon usage variation is considered to be an indicator of the type of force that influences genome evolution. Investigation of codon bias and the forces that influence it provides insights into the fundamental mechanisms of viral evolution. Understanding codon bias is essential to understand the interplay between a virus and its host
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