ArticlePloS one2013
Synonymous codon usage in TTSuV2: analysis and comparison with TTSuV1.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Reassessing Murinae phylogeny: integrated mitogenomic and codon usage evidence challenges the sister relationship of Micromyini and Vernayini.BMC genomics · 2026Article
- The completed mitochondrial genomes of Globodera vulgaris reveals new insights into the genus Globodera phylogeny.Scientific reports · 2024Article
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- Analysis of codon usage patterns in open reading frame 4 of hepatitis E viruses.Beni-Suef University journal of basic and applied sciences · 2022Article
- Compositional Features and Codon Usage Pattern of Genes Associated with Anxiety in Human.Molecular neurobiology · 2020Article
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- Codon usage pattern and its influencing factors in different genomes of hepadnaviruses.Archives of virology · 2020Article
- Distinctive features gleaned from the comparative genomes analysis of clinical and non-clinical isolates of Klebsiella pneumoniae.Bioinformation · 2020Article
- Compositional properties and codon usage pattern of mitochondrial ATP gene in different classes of Arthropoda.Genetica · 2019Article
- Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus.International journal of molecular sciences · 2019Article
- Analysis of codon usage patterns and influencing factors in Nipah virus.Virus research · 2019Article
- Codon Usage Pattern of Genes Involved in Central Nervous System.Molecular neurobiology · 2019Article
- Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome.Genetica · 2017Article
- Nucleotide composition bias and codon usage trends of gene populations in Mycoplasma capricolum subsp. capricolum and M. Agalactiae.Journal of genetics · 2015Article
- On the biased nucleotide composition of the human coronavirus RNA genome.Virus research · 2015Article
- Codon bias and gene expression of mitochondrial ND2 gene in chordates.Bioinformation · 2015Article
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Authors and funding
3 authors.
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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.
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