Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function
<p>Abstract</p> <p>Background</p> <p>Complete genome sequences of the <it>Astroviridae </it>include human, non-human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full-length genomes a...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2007-03-01
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| Series: | Virology Journal |
| Online Access: | http://www.virologyj.com/content/4/1/25 |
| Summary: | <p>Abstract</p> <p>Background</p> <p>Complete genome sequences of the <it>Astroviridae </it>include human, non-human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full-length genomes and from non-synonymous nucleotide substitutions in each of the three ORFs. Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species.</p> <p>Results</p> <p>We analyzed the complete <it>Astroviridae </it>family for the inference of adaptive molecular evolution at sites and in branches. High rates of synonymous mutations are observed among the non-human virus species. Deviant patterns of synonymous substitutions are found in the capsid structural genes. Purifying selection is a dominant force among all astrovirus genes and only few codon sites showed values for the dN/dS ratio that may indicate site-specific molecular adaptation during virus evolution. One of these sites is the glycine residue of a RGD motif in ORF2 of human astrovirus serotype 1. RGD or similar integrin recognition motifs are present in nearly all astrovirus species.</p> <p>Conclusion</p> <p>Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS. Sites with enhanced values for dN/dS are prominent at domains in charge of environmental communication (f.i. VP27 and domain 4 in ORF1a) more than at domains dedicated to intrinsic virus functions (f.i. VP34 and ORF1b (the virus polymerase)). Integrin recognition may play a key role in astrovirus to target cell attachment.</p> |
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| ISSN: | 1743-422X |