Phylogenetic analysis and signature of recombination hotspots in sugarcane mosaic virus infecting sugarcane in India

Abstract

Sugarcane mosaic virus (SCMV) one of the causative viruses of mosaic disease in sugarcane occurs in sugarcane growing countries worldwide. India is the second largest sugarcane producing country and genome of SCMV from India has not been characterized so far. Hence detailed studies were carried out to characterize the virus isolates based on its complete genome. Comparative genome analyses of five new isolates were performed with previously reported SCMV full genome sequences of isolates infecting sugarcane, maize, sorghum and Canna. Sequence identity matrix and phylogenetic analyses clearly represented that Indian isolates are closely related to sugarcane infecting isolates reported from Australia, Argentina, China and Iran and they diverged as a separate subgroup from other reported maize infecting isolates from Mexico, China, Ohio, Spain, Germany, Iran, Ethiopia, Kenya and Eucador. Selection pressure analysis clearly depicted the predomination of strong purifying selection throughout the viral genome, and strongest in CI and HC-Pro gene. Evidence for few positively selected sites was identified in all the cistrons except in 6 K1 and Nib rep. Among the genomic region, CI gene has exhibited comparatively more recombination hotspots followed by HC-Pro unlike other reported isolates. As the cultivation of sugarcane first originated in India, our results from the recombination events strongly suggest that Indian SCMV populations contribute for the emergence of upcoming new recombinant SCMV isolates not only within the sugarcane isolates but also with maize infecting isolates of SCMV in other countries irrespective of geographic origin and host type.