Genetic diversity and population structure of Sugarcane mosaic virus

Sugarcane mosaic virus (SCMV) is one of the causal pathogens of mosaic diseases on sugarcane, maize, sorghum and some other graminaceous species with worldwide distribution. The global genetic diversity and molecular evolution of SCMV capsid protein (CP) gene were investigated with the nucleotide sequences available in the GenBank database. Phylogenetic analyses revealed that SCMV isolates clustered in relation to their original hosts, and geographically distinct isolates from maize or sugarcane clustered differently. The populations between maize and sugarcane showed frequent gene flows; but within maize or sugarcane geography distinct isolates had infrequent gene flow. Recombination existed in the region of CP cistron and 3′-untranslated region (UTR). Most of the codons in the CP gene were under negative selection or neutral evolution except for codons 27 and 48, which were under positive selection. This study provided systematic analyses of the evolutionary processes contributing to the observed diversification of SCMV populations.