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Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1

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...

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Autores principales: Zhang, Zhicheng, Dai, Wei, Dai, Dingzhen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841265/
https://www.ncbi.nlm.nih.gov/pubmed/24303050
http://dx.doi.org/10.1371/journal.pone.0081469
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author Zhang, Zhicheng
Dai, Wei
Dai, Dingzhen
author_facet Zhang, Zhicheng
Dai, Wei
Dai, Dingzhen
author_sort Zhang, Zhicheng
collection PubMed
description 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.
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spelling pubmed-38412652013-12-03 Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1 Zhang, Zhicheng Dai, Wei Dai, Dingzhen PLoS One Research Article 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. Public Library of Science 2013-11-26 /pmc/articles/PMC3841265/ /pubmed/24303050 http://dx.doi.org/10.1371/journal.pone.0081469 Text en © 2013 Zhang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Zhang, Zhicheng
Dai, Wei
Dai, Dingzhen
Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1
title Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1
title_full Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1
title_fullStr Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1
title_full_unstemmed Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1
title_short Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1
title_sort synonymous codon usage in ttsuv2: analysis and comparison with ttsuv1
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841265/
https://www.ncbi.nlm.nih.gov/pubmed/24303050
http://dx.doi.org/10.1371/journal.pone.0081469
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