Sequence analysis of RNA3 of <em>Maize stripe virus</em> associated with stripe disease of sorghum (<em>Sorghum bicolor</em>) in India

Abstract

Maize stripe virus (MSpV), one of the distinct species of the genus Tenuivirus, has been associated with stripe disease of sorghum in India. In this study, we report the complete sequence analysis of ambisense RNA3 of four MSpV isolates associated with this disease, to confirm its correct identity. The RNA3 of four MSpV-Sorg isolates is 2357 nucleotides in length with two ORFs, one in virion sense (594 nucleotides, non-structural protein 3, NS3) and the other in complementary sense (951 nucleotides, coat protein, CP). The intergenic region between these two ORFs is 653 nucleotides in length, which is rich in U and A residues. The deduced molecular weights of NS3 and CP are ≈22 and ≈34 kDa, respectively. RNA3 has ≈82% sequence identity at nucleotide level with RNA3 of MSpV infecting maize in Florida, USA and Reunion. NS3 and CP ORFs shared ≈94% and ≈95% identities at amino acid levels, respectively with MSpV isolates of maize from Florida and Reunion. The internal non-coding region between two ORFs has 67–68% identity at nucleotide level with the reported MSpV isolates from Florida and Reunion. The sequence identity was more than ≈98% among the four isolates of MSpV-Sorg. Compared to maize-infecting MSpV isolates in USA and Reunion, the sorghum-infecting MSpV isolates in India had more amino acid substitutions in both NS3 and CP. This is the first report of complete sequence analysis of MSpV RNA3 from Asia.