Population Genetics, Synonymous Codon Usage & Evolution Of Begomoviruses

Begomovirus are the genus with majority members in the family Geminiviridae with wide distribution and host range and cause many diseases. Begomoviruses have circular single-stranded DNA (ssDNA) genomes encapsidated within twinned particles. Because of the severe damage to important crops such as tomato, cassava and cotton in the world, and the corresponding huge losses of agricultural production, the occurence, transmission, genome structure and function, genetic characteristics and evolution of begomoviruses have been becoming a hot research field. Tomato yellow leaf curl virus (TYLCV) in the Begomovirus genus spread very rapidly in the World and cause devastating diseases in tomato. TYLCV causes tomato yellow leaf curl diseases (TYLCD) with visual symptoms such as curling, yellowing and reduction of the leavlets area together with stunting and so on. A number of begomovirus isolates have been collected from Yunnan and Guangxi provinces in southwest of China, and seqence analysis indicated Tomato yellow leaf curl China virus (TYLCCNV) occurred widely in these regions.The complete nucleotide sequences of sixteen TYLCCNV isolates collected from six sites in the Yunnan and Guangxi provinces in southwest of China from 1999 to 2005, together with other two isolates in GenBank were used in our population genetic investigation. The phylogenetic analysis of the TYLCCNV 18 isolates strongly suggested a geography-related genetic variation or diversity. No significant genetic variation and diversity was detected among TYLCCNV isolates collected from different hosts or different times. The results suggest that geographical selection force plays important role in TYLCCNV evolution while host and time have relative weak effect. Moreover, occurrence of TYLCCNV population expansions and the high frequency of recombination among the TYLCCNV genomes was also documented. The intraspecific genetic diversity of TYLCCNV was also examined at all sites for genomes and their coding regions. It was found that the high genetic diversity was located at non-coding or non-overlapped coding regions, rather than coding or overlapped coding sequences. The genetic diversity pattern indicated that the selective constraints (or pressures) were lower in non-coding or non-overlapped coding regions, where it might become the potential mutation hotspots. The analysis of genetic diversity between the two intergenic regions flanking AC1 and AV2 (IR2 and IR1) suggested the potential different roles or functions between them.The analysis on codon usage suggested that, apart from base mutation bias, other factors such as selection pressure might also play a role in shaping the codon usage bias of begomoviruses. Further analysis indicated that the codon usage of AC4 genes was actually shaped by the base mutation bias derived from AC1 genes, not determined visually by the selection pressures. Taken together, it was suggested that the synonymous codon usage variation of begomoviruses was mainly influenced by base mutation bias. Analysis on the base composition of the begomovirus genes showed that the two genes of AV1 (V1) and BV1 had relatively stronger synonymous codon usage bias and higher expression level. It also showed that AV1 gene didn't tend to use A (Trending or G (C)-ending codons and, however, tended to use T-ending codons in comparison with A-ending codons. Thus, 14 codons were finally determined as optimal ones with regard to the higher expression genes AV1 (V1) as a reference set. Analysis of the codon usage patterns of begomoviruses with different hosts suggested that begomoviruses infected tomato more adaptively than other hosts such as cassava and ageratum. Furthermore, there was no correlation between the synonymous codon usage patterns of geminiviruses and the appeared symptoms for corresponding hosts after being infected. In addition, the apparent differences of the codon usage patterns between the Old World monopartite viruses and the New World bipartite viruses, indicated that the New World bipartite viruses probably evolved from the Old World bipartite ones, which were evolved from the Old World monopartite viruses. The comparative analysis between begomoviruses and other three genera of geminiviruses suggested that apart from the genus Mastrevirus, other geminiviruses had the same codon usage patterns. In addition, the function-alike genes from different genera of geminiviruses also had the similar patterns of codon usage, which indicated the codon usage of plant viruses had a certain functional implication. In general, monocots and dicots have distinguishable codon bias. Correspodence analysis and cluster analysis based on codon usage indices also indicated that the mono- and dico-infectiong geminiviruses had the apparent variations in codon usage. The results suggested that the synonymous codon usage patterns of different geminiviruses were also influenced by the environment where their hosts stay, showing a certain extent of host-specific.