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Heterogeneity in codon usages of sobemovirus genes
1Natural Environmental Research Council/Centre for Ecology and Hydrology Oxford, Oxford, UK.
Archives of Virology
|April 19, 2005
Summary
Sobemoviruses, plant viruses, show distinct monocot-infecting and dicot-infecting lineages. Relative Synonymous Codon Usage (RSCU) analysis suggests these viruses, particularly their replicase gene, originated from monocot hosts.
Area of Science:
- Virology
- Molecular Evolution
- Bioinformatics
Background:
- Sobemoviruses are plant viruses with two known lineages: those infecting monocots and those infecting dicots.
- Phylogenetic analysis of 14 genome sequences revealed these two distinct sobemovirus groups.
Purpose of the Study:
- To investigate the evolutionary origin of sobemoviruses, specifically whether they originated from monocot or dicot hosts.
- To compare the effectiveness of phylogenetic trees and Relative Synonymous Codon Usage (RSCU) trees in classifying sobemoviruses.
Main Methods:
- Construction of phylogenetic trees using 14 sobemovirus genome sequences.
- Construction of relationship trees based on Relative Synonymous Codon Usage (RSCU) of viral sequences.
- Comparison of viral codon usage with that of monocot and dicot host species.
- Calculation of RSCU values for individual viral open reading frames (ORFs), particularly ORF-2 encoding the replicase.
Main Results:
- RSCU-based trees provided better separation of monocot- and dicot-infecting sobemoviruses than genome phylogenetic trees.
- When host species were incorporated into RSCU trees, sobemoviruses clustered with monocot hosts, indicating codon usage similarities.
- The codon usage of viral ORF-2 (replicase) showed a stronger affinity to plant sequences compared to other viral ORFs.
- ORF-2 from most sobemoviruses, regardless of their host, exhibited greater RSCU similarity to monocot sequences than dicot sequences.
Conclusions:
- Relative Synonymous Codon Usage (RSCU) is a valuable tool for studying viral evolution and host associations.
- The codon usage patterns of sobemoviruses, especially their replicase gene (ORF-2), suggest a monocot origin for the genus Sobemovirus.
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