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Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus

The torque teno sus virus (TTSuV) is an emerging virus threating the Suidae species of unclear pathogenicity, although it was previously reported as a worsening factor of other porcine diseases, in particular, porcine circovirus associated disease (PCVAD). Here, a comprehensive codon usage analysis...

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Autores principales: Li, Gairu, Zhang, Wenyan, Wang, Ruyi, Xing, Gang, Wang, Shilei, Ji, Xiang, Wang, Ningning, Su, Shuo, Zhou, Jiyong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628323/
https://www.ncbi.nlm.nih.gov/pubmed/31200479
http://dx.doi.org/10.3390/ijms20122881
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author Li, Gairu
Zhang, Wenyan
Wang, Ruyi
Xing, Gang
Wang, Shilei
Ji, Xiang
Wang, Ningning
Su, Shuo
Zhou, Jiyong
author_facet Li, Gairu
Zhang, Wenyan
Wang, Ruyi
Xing, Gang
Wang, Shilei
Ji, Xiang
Wang, Ningning
Su, Shuo
Zhou, Jiyong
author_sort Li, Gairu
collection PubMed
description The torque teno sus virus (TTSuV) is an emerging virus threating the Suidae species of unclear pathogenicity, although it was previously reported as a worsening factor of other porcine diseases, in particular, porcine circovirus associated disease (PCVAD). Here, a comprehensive codon usage analysis of the open reading frame 1 (ORF1), which encodes the viral capsid protein, was undertaken for the first time to reveal its evolutionary history. We revealed independent phylogenetic processes for the two genera during TTSuV evolution, which was confirmed by principal component analysis (PCA). A low codon usage bias was observed in different genera and different species, with Kappatorquevirus a (TTSuVk2a) displaying the highest, which was mainly driven by mutation pressure and natural selection, especially natural selection. Overall, ATs were more abundant than GCs, along with more A-ended synonymous codons in relative synonymous codon usage (RSCU) analysis. To further confirm the role of natural selection and TTSuV adaptation to the Suidae species, codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses were performed, which showed different adaptations for different TTSuVs. Importantly, we identified a more dominant role of Sus scrofa in the evolution of Iotatorquevirus (TTSuV1), with the highest CAI values and lowest RCDI values compared to Sus scrofa domestica. However, in TTSuVk2, the roles of Sus scrofa and Sus scrofa domestica were the same, regarding codon usage, with similar CAI and RCDI values. Our study provides a new perspective of the evolution of TTSuV and valuable information to develop control measures against TTSuV.
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spelling pubmed-66283232019-07-23 Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus Li, Gairu Zhang, Wenyan Wang, Ruyi Xing, Gang Wang, Shilei Ji, Xiang Wang, Ningning Su, Shuo Zhou, Jiyong Int J Mol Sci Article The torque teno sus virus (TTSuV) is an emerging virus threating the Suidae species of unclear pathogenicity, although it was previously reported as a worsening factor of other porcine diseases, in particular, porcine circovirus associated disease (PCVAD). Here, a comprehensive codon usage analysis of the open reading frame 1 (ORF1), which encodes the viral capsid protein, was undertaken for the first time to reveal its evolutionary history. We revealed independent phylogenetic processes for the two genera during TTSuV evolution, which was confirmed by principal component analysis (PCA). A low codon usage bias was observed in different genera and different species, with Kappatorquevirus a (TTSuVk2a) displaying the highest, which was mainly driven by mutation pressure and natural selection, especially natural selection. Overall, ATs were more abundant than GCs, along with more A-ended synonymous codons in relative synonymous codon usage (RSCU) analysis. To further confirm the role of natural selection and TTSuV adaptation to the Suidae species, codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses were performed, which showed different adaptations for different TTSuVs. Importantly, we identified a more dominant role of Sus scrofa in the evolution of Iotatorquevirus (TTSuV1), with the highest CAI values and lowest RCDI values compared to Sus scrofa domestica. However, in TTSuVk2, the roles of Sus scrofa and Sus scrofa domestica were the same, regarding codon usage, with similar CAI and RCDI values. Our study provides a new perspective of the evolution of TTSuV and valuable information to develop control measures against TTSuV. MDPI 2019-06-13 /pmc/articles/PMC6628323/ /pubmed/31200479 http://dx.doi.org/10.3390/ijms20122881 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Li, Gairu
Zhang, Wenyan
Wang, Ruyi
Xing, Gang
Wang, Shilei
Ji, Xiang
Wang, Ningning
Su, Shuo
Zhou, Jiyong
Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus
title Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus
title_full Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus
title_fullStr Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus
title_full_unstemmed Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus
title_short Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus
title_sort genetic analysis and evolutionary changes of the torque teno sus virus
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628323/
https://www.ncbi.nlm.nih.gov/pubmed/31200479
http://dx.doi.org/10.3390/ijms20122881
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