Genomic characterization and phylogenetic analysis of Cucumber Mosaic Virus infecting Chilli in Telangana

Abstract

Cucumber Mosaic Virus (CMV) is one of the most widespread and economically destructive plant viruses affecting vegetable crops such as chilli, tomato, and cucumber in India. The present study aimed to elucidate the evolutionary and molecular diversity of CMV isolates infecting chilli crops in Telangana. Field samples showing typical CMV symptoms were collected from major chilli-growing districts including Hyderabad,
Mahaboonagar, Warangal, Nalgonda, and Khammam. Complete genome sequencing of these five isolates revealed the tripartite RNA genome organization of CMV, with genome sizes of RNA1 ranging from 3339– 3358 nt, RNA2 from 3044–3056 nt, and RNA3 from 2207–2222 nt. Comparative analyses showed that the genome architecture of the Telangana isolates closely resembled that of 44 CMV isolates reported globally. Nucleotide sequence identity among the TEL isolates and other CMV global isolates ranged from 88.1– 99.7% for RNA1, 88.6–99.6% for RNA2, and 89–99.6% for RNA3, indicating a high level of conservation. Cistron-by-cistron analysis, including both coding and untranslated regions (UTRs), exhibited similar sequence identity trends. Phylogenetic analysis based on the full-length genomes and individual RNA
segments grouped global CMV isolates into three major subgroups: IA, IB, and II. All the TEL isolates from Telangana consistently clustered within subgroup IB, suggesting their close evolutionary relationship with CMV subgroup IB strains reported from different geographical regions. This study provides the first comprehensive genomic characterization of CMV isolates infecting chilli in Telangana and contributes
valuable insights into the evolutionary dynamics, genetic variability, and phylogenetic placement of CMV populations in India.