Complex diversityin papaya ringspot virus (PRSV) populations is governed by the host species and the geo-climatic locations
Year: 2026
Type: preprint
Abstract: Papaya ringspot virus (PRSV) is one of the most important viral pathogens limiting papaya and cucurbit production globally. However, the evolutionary processes governing its population structure across diverse agro-ecological environments remain insufficiently understood. This study examined the genetic diversity, recombination patterns, and population structure of PRSV-P and PRSV-W isolates collected from different hosts and geo-climatic regions of India. Twenty-seven PRSV isolates originated from papaya and multiple cucurbit species were analyzed based onthe sequences of three protein coding regions: helper component proteinase (HC-Pro), nuclear inclusion proteinase-a (NIa-Pro), and coat protein (CP). The CP gene displayed substantial variation, ranging from 837 to 876 nucleotides, with the amino acid (aa)sequence diversities reaching up to 20%. Higher diversity was observed among cucurbit-derived PRSV-P isolates from warm semi-arid (WSA) regions, primarily through frequent aainsertion and deletion events. Phylogenetic analyses revealed varying evolutionary patterns among genomic regions. CP sequences grouped according to geo-climatic origin, whereas NIa-Pro differentiated based on host-& pathotype-associated lineages (PRSV-P and PRSV-W), while HC-Pro showed no distinct clustering patterns. Recombination analysis identified gene-specific evolutionary dynamics, with recombination detected in CP and NIa-Pro but not in HC-Pro. Population genetic analyses indicated extremely high haplotype diversity ( Hd = 0.996), strong population subdivision ( Snn = 0.88889–1.00000; p ≤ 0.004), and moderate to high genetic differentiation ( Fst = 0.1899–0.7713), despite restricted gene flow ( Nm = 0.20). Negative Tajima’s D values suggested recent population expansion and/or strong purifying selection. Overall, environmental variation, host association, and gene-specific constraints jointly influence PRSV evolution, while genetic isolation and limited gene flow promote diversification and ecological adaptation across distinct geo-climatic regions.
Source: Research Square
Institutions: Indian Agricultural Research Institute, Amity University
Language: English
Topic: Plant Virus Research Studies
Subfield: Plant Science
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7225736623