Global Analysis of Rice Tungro Spherical Virus Coat Proteins Reveals New Roles in Evolutionary Consequences

Rice tungro disease is caused by a combination of two viruses: Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). RTSV has a capsid comprising three coat proteins (CP) species. Three CP genes of RTSV-AP isolate were sequenced and compared with 9 other isolates reported worldwide for their phylogenetic survey of recombination events which revealed that in general Indian isolates are forming one separate cluster while those of Philippines and Malaysia forming a different cluster. A significant proportion of recombination sites were found in the CP1 gene, followed by CP2 and CP3 suggesting that it is a major phenomenon in the evolution of various isolates of RTSV. Some interesting domains and motifs such as; 3,4-dihydroxy-2-butanone 4-phosphate synthase in CP1, Type 1 glutamine amidotransferase domain and RNA binding motifs in CP2, domains of receptor proteins in CP3, and glycosylation motif in CP2 and CP3 were also obtained in RTSV coat protein. In addition, simple modular architecture research tool (SMART) analysis of coat proteins of RTSV predicted the coat protein domain of calicivirus suggesting evolutionary linkages between plant and animal viruses. This study provides an opportunity to establish the molecular evolution and sequence-function relationship of RTSV.