Genetic diversity and evolutionary relationships of Sugarcane mosaic virus variants

Abstract

Sugarcane mosaic virus (SCMV) belongs to genus Potyvirus (family Potyviridae). It is non-enveloped, rod shaped flexuous and filamentous positive sense RNA of approximately 750 nanometer in length. SCMV is responsible for causing mosaic disease in sugarcane, sorghum, maize and other Poaceous plants. Present study is aimed at to explore the genetic diversity and evolutionary relationships among various isolates of SCMV. Seventy-nine full length sequences of SCMV has been retrieved from databases and characteristics of genome were determined. Sequence features, recombination analysis, and phylogenetic relationships were performed through MatGat, RDP4, MEGA, Geneious and Bayesian matrix, respectively. Sequences size of SCMV full genome were between 9549 to 9640 nucleotides (nt) and between 3063 to 3078 amino acids. Total number of nucleotides for P1 were 698 to 732 nt while for CP nucleotides were 980 to 985 nt. The sequences of P1, CP and full genome shared nucleotide identity between 76%-100%, 58%-100% and 76%-100%, respectively while amino acid sequence identity showed between 82%- 100%, 58%-100%, and 80%-100%, respectively. The ranges of the sequence identity for P1, CP and full length are in accordance with species demarcation criteria given by ICTV. Recombination was not observed in CP region, while full genome sequences from Iran and China has shown several recombination events. Hot spots for recombination in SCMV are 6K1, Vpg, NIa-Pro and NIb. Phylogenetic trees of P1, CP and full genome sequences was constructed using Maximum likelihood method and verified through Bayesian analysis. The position of isolates in trees generated from P1, CP and full-length sequence were different the trees. Comparative analysis of individual genes and full genome shows three patterns of SCMV evolution. The first pattern reflected geographical based distribution, second pattern observed host dependent classification variation lies in presence of additional 20 nucleotide bases stretch in sequences from host maize, recombination-based pattern is observed in third pattern of evolution. The high levels of identity observed between isolates obtained from distant geographic areas could be explained by movement of maize germplasm since SCMV can be seed transmitted. Recombination plays an important role in virus evolution and emergence of new species/strains. Based on recombination and phylogenetic analysis, it is concluded that full length genome should be considered for classification and determination of evolutionary relationships. Full genome sequence data are crucial to determine biology, diversity and evolutionary history of a virus, for devising new control strategies and evaluating its risk. The results of this study will add new insights to the current knowledge of the SCMV evolution and genetic diversity in the world.