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Clustering of classical swine fever virus isolates by codon pair bias
BACKGROUND: The genetic code consists of non-random usage of synonymous codons for the same amino acids, termed codon bias or codon usage. Codon juxtaposition is also non-random, referred to as codon context bias or codon pair bias. The codon and codon pair bias vary among different organisms, as we...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3341591/ https://www.ncbi.nlm.nih.gov/pubmed/22126254 http://dx.doi.org/10.1186/1756-0500-4-521 |
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author | Leifer, Immanuel Hoeper, Dirk Blome, Sandra Beer, Martin Ruggli, Nicolas |
author_facet | Leifer, Immanuel Hoeper, Dirk Blome, Sandra Beer, Martin Ruggli, Nicolas |
author_sort | Leifer, Immanuel |
collection | PubMed |
description | BACKGROUND: The genetic code consists of non-random usage of synonymous codons for the same amino acids, termed codon bias or codon usage. Codon juxtaposition is also non-random, referred to as codon context bias or codon pair bias. The codon and codon pair bias vary among different organisms, as well as with viruses. Reasons for these differences are not completely understood. For classical swine fever virus (CSFV), it was suggested that the synonymous codon usage does not significantly influence virulence, but the relationship between variations in codon pair usage and CSFV virulence is unknown. Virulence can be related to the fitness of a virus: Differences in codon pair usage influence genome translation efficiency, which may in turn relate to the fitness of a virus. Accordingly, the potential of the codon pair bias for clustering CSFV isolates into classes of different virulence was investigated. RESULTS: The complete genomic sequences encoding the viral polyprotein of 52 different CSFV isolates were analyzed. This included 49 sequences from the GenBank database (NCBI) and three newly sequenced genomes. The codon usage did not differ among isolates of different virulence or genotype. In contrast, a clustering of isolates based on their codon pair bias was observed, clearly discriminating highly virulent isolates and vaccine strains on one side from moderately virulent strains on the other side. However, phylogenetic trees based on the codon pair bias and on the primary nucleotide sequence resulted in a very similar genotype distribution. CONCLUSION: Clustering of CSFV genomes based on their codon pair bias correlate with the genotype rather than with the virulence of the isolates. |
format | Online Article Text |
id | pubmed-3341591 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-33415912012-05-02 Clustering of classical swine fever virus isolates by codon pair bias Leifer, Immanuel Hoeper, Dirk Blome, Sandra Beer, Martin Ruggli, Nicolas BMC Res Notes Research Article BACKGROUND: The genetic code consists of non-random usage of synonymous codons for the same amino acids, termed codon bias or codon usage. Codon juxtaposition is also non-random, referred to as codon context bias or codon pair bias. The codon and codon pair bias vary among different organisms, as well as with viruses. Reasons for these differences are not completely understood. For classical swine fever virus (CSFV), it was suggested that the synonymous codon usage does not significantly influence virulence, but the relationship between variations in codon pair usage and CSFV virulence is unknown. Virulence can be related to the fitness of a virus: Differences in codon pair usage influence genome translation efficiency, which may in turn relate to the fitness of a virus. Accordingly, the potential of the codon pair bias for clustering CSFV isolates into classes of different virulence was investigated. RESULTS: The complete genomic sequences encoding the viral polyprotein of 52 different CSFV isolates were analyzed. This included 49 sequences from the GenBank database (NCBI) and three newly sequenced genomes. The codon usage did not differ among isolates of different virulence or genotype. In contrast, a clustering of isolates based on their codon pair bias was observed, clearly discriminating highly virulent isolates and vaccine strains on one side from moderately virulent strains on the other side. However, phylogenetic trees based on the codon pair bias and on the primary nucleotide sequence resulted in a very similar genotype distribution. CONCLUSION: Clustering of CSFV genomes based on their codon pair bias correlate with the genotype rather than with the virulence of the isolates. BioMed Central 2011-11-29 /pmc/articles/PMC3341591/ /pubmed/22126254 http://dx.doi.org/10.1186/1756-0500-4-521 Text en Copyright ©2011 Leifer et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Leifer, Immanuel Hoeper, Dirk Blome, Sandra Beer, Martin Ruggli, Nicolas Clustering of classical swine fever virus isolates by codon pair bias |
title | Clustering of classical swine fever virus isolates by codon pair bias |
title_full | Clustering of classical swine fever virus isolates by codon pair bias |
title_fullStr | Clustering of classical swine fever virus isolates by codon pair bias |
title_full_unstemmed | Clustering of classical swine fever virus isolates by codon pair bias |
title_short | Clustering of classical swine fever virus isolates by codon pair bias |
title_sort | clustering of classical swine fever virus isolates by codon pair bias |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3341591/ https://www.ncbi.nlm.nih.gov/pubmed/22126254 http://dx.doi.org/10.1186/1756-0500-4-521 |
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