Evolutionary Analysis Of Turnip Mosaic Virus Genomic Sequences Based On Synonymous Codon Usage

Codon analysis and its application in bioimformatics and evolutionary studies are important issues for investigating the genome evolution, protein function and inter-action between genetics and environment. The majority of prokaryotic and eukaryotic species have a non-random codon usage. Alternative synonymous codons in most genes are used with unequal frequency. Certain synonymous codons are significantly preferred over others. Synonymous codon usage analysis is useful to find some genomic features and to understand the molecular evolution of genomes. Most researches on the codon usage focused on the autotrophic organisms not paratrophic ones, like viruses. Resent data showed that the codon usage of viral genes does not completely match with their hosts. It indicated that codon usage plays an important role in the interaction between viruses and their hosts. But the studies of plant virus are rare. Here we focused on the characters of codon usage of Turnip mosaic virus (TuMV), factors which influencing the viral codon. We analyze Synonymous codon usage patterns and underlying driving forces among different genomes within species of Turnip mosaic virus (TuMV).Turnip mosaic virus (TuMV) is a very important member of Potyvirus. Full genome sequences of 92 Turnip mosaic virus (TuMV) isolates have been reported in the GenBank, 58 out of which were reported to be non-recombinants. We caculated the relative synonymous codon usage of 90 TuMV genes coding for P1, CP protein and clustered it into four categories by using the method of hierarcial cluster analysis. The phylogenetic relationships based on amino acid replacements of these 90 TuMV genes can be clustered into four categories too. The results show that based on these two different models have no great relevance. Then, the Codon usage bias has been investigated on these 92 and 58 TuMV completely genome sequences isolates using the method of hierarcial cluster analysis. The phylogenetic relationships based on nucleotide sequences of these 92 and 58 TuMV isolates were analyzed too. Results show that the codon usage patterns of those 58 TuMV isolates are found to be significantly phylogenetically conserved and almost consistent with the host type. These results suggested that in the condition of no recombination codon usage bias may be one of the host selective pressures affecting the point mutation of TuMV genome in its adaptation to the niche in their host.We caculated the relative synonymous codon usage, Nc, GC3s of other kind of potyvirus isolates to compare with TuMV. The results show that codon usage preferences of potyvirus are species different.