Genetic variation of coat protein gene among the isolates of Rice tungro spherical virus from tungro-endemic states of the India Satendra K. Mangrauthia • P. Malathi • Surekha Agarwal • G. Ramkumar • D. Krishnaveni • C. N. Neeraja • M. Sheshu Madhav • D. Ladhalakshmi • S. M. Balachandran • B. C. Viraktamath Received: 10 November 2011 / Accepted: 21 December 2011 / Published online: 11 January 2012 Ó Springer Science+Business Media, LLC 2012 Abstract Rice tungro disease, one of the major con- straints to rice production in South and Southeast Asia, is caused by a combination of two viruses: Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). The present study was undertaken to determine the genetic variation of RTSV population present in tungro endemic states of Indian subcontinent. Phylogenetic anal- ysis based on coat protein sequences showed distinct divergence of Indian RTSV isolates into two groups; one consisted isolates from Hyderabad (Andhra Pradesh), Cuttack (Orissa), and Puducherry and another from West Bengal, Coimbatore (Tamil Nadu), and Kanyakumari (Tamil Nadu). The results obtained from phylogenetic study were further supported with the SNPs (single nucleotide polymorphism), INDELs (insertion and dele- tion) and evolutionary distance analysis. In addition, sequence difference count matrix revealed 2–68 nucleo- tides differences among all the Indian RTSV isolates taken in this study. However, at the protein level these differ- ences were not significant as revealed by Ka/Ks ratio cal- culation. Sequence identity at nucleotide and amino acid level was 92–100% and 97–100%, respectively, among Indian isolates of RTSV. Understanding of the population structure of RTSV from tungro endemic regions of India would potentially provide insights into the molecular diversification of this virus. Keywords RTSV Á CP Á Phylogeny Á Diversity Á Identity Introduction Rice tungro disease (RTD) causes severe yield losses worldwide. When plants are infected with RTD in the early seedling stage, yield losses can be as high as 100% [1, 2]. Tungro is a complex disease comprising of two unrelated virus particles viz., Rice tungro bacilliform virus (RTBV) with double-stranded DNA genome and Rice tungro spherical virus (RTSV) with single-stranded RNA genome [3]. A disease resulting from co-infection by RTBV and RTSV causes disease symptoms such as stunting and dis- coloration of infected plants, reduced tillering, and small and/or sterile panicles. Plants infected with RTBV and RTSV show typical tungro symptoms, whereas, plants infected with RTBV alone show very mild yellowing and stunting. RTBV is responsible for symptom development, whereas RTSV is responsible for the transmission of viral complex by green leaf hoppers [4]. RTSV, a member of the family Sequiviridae, has a polyadenylated single-stranded RNA genome of about 12 kb that is encapsidated within isometric particles [5]. The genome encodes a single large ORF of *3,473 amino acids [6]. There are three coat protein subunits, CP1, CP2, and CP3, with predicted molecular masses of 22.5, 22.0, and 33.0 kDa, respec- tively, which are cleaved from polyprotein [7]. There have been numerous efforts to understand the genetic diversity of RTBV in India [8–10], however, very S. K. Mangrauthia (&) Á P. Malathi Á S. Agarwal Á G. Ramkumar Á C. N. Neeraja Á M. S. Madhav Á S. M. Balachandran Biotechnology Section, Directorate of Rice Research, Hyderabad, Andhra Pradesh 500030, India e-mail: skmdrr@gmail.com D. Krishnaveni Á D. Ladhalakshmi Division of Plant Pathology, Directorate of Rice Research, Hyderabad, Andhra Pradesh 500030, India B. C. Viraktamath Directorate of Rice Research, Hyderabad, Andhra Pradesh 500030, India 123 Virus Genes (2012) 44:482–487 DOI 10.1007/s11262-011-0708-3