Emergence of novel Sugarcane bacilliform virus genotypes with evidences of recombination

Abstract

To explore the genetic diversity in SCBV, samples from 125 germplasm and 233 cultivated varieties were collected during the 2019-20 from different places of Tamil Nadu, Kerala, Karnataka, Maharashtra, Andaman and Nicobar islands. Germplasm clones comprised of Saccharum officinarum, S. spontaneum, S. barberi, S. sinense, Erianthus arundinaceus; cultivars included Saccharum hybrid varieties, Saccharum inter specific hybrid varieties and exotic clones. Phylogenetic analysis of the sequences revealed formation of three major groups, in which most of the isolates clustered in 3rd monophyletic group. Apart from the known 20 genotypes, 4 novel genotypes were discovered from the study such as SCBV-U, SCBV-V, SCBV-W and SCBV X. About 56 SCBV isolates from the study were grouped into a separate major cluster forming a new genotype SCBV-U. Another 16 isolates formed a new branch SCBV-V. The isolate CBJ46 alone formed a distinct branch (SCBV-W) outside the 3rd monophyletic tree, because of the sequence dissimilarities compared with other isolates from the study. This variant can be even considered as a new species, but it necessitates complete analysis of the genome. S. officinarum clones (Bangadya, Saipan G, Baragua); S. spontaneum 81-095; ISH 1 and Cym 08-666 formed a diverse cluster forming a novel genotype SCBV X. From published genotypes, the following genotypes were reported for first time from India viz., SCBV-G (France and China), SCBV-Q (China), SCBV-R (China) and SCBV-S (China). RDP4 recombination analysis suggested 19 recombinants from the study; MS 901, CB 96007, S. officinarum Khajuria and CBSe 95436 were major potent recombinants where default P- value used was 0.05. SCBV-U, a novel genotype from the present study can be considered as the commonly occurring genotype in India especially in case of isolates from Saccharum hybrids. Analyzing large number of germplasm clones may reveal all possible genotypes of SCBV; thus ease the process of virus indexing and also lend a hand in molecular diagnostics. Phylogenetic analysis, recombination patterns and the knowledge about hot spots found in the RT/RNase H region of SCBV species can help to find the evolution within the species happened over the years. Present study provides a major portrayal of the prevalence, distribution and genetic diversity of the SCBV species complex in India