Genomic Characterization and Comparative Evolutionary Analysis of Pepper Yellow Leaf Curl Viruses in Southeast Asia

Abstract

Pepper yellow leaf curl Indonesia virus (PepYLCIV), a bipartite begomovirus transmitted by Bemisia tabaci, is a major viral pathogen affecting chili pepper production in Indonesia. Although complete genome sequences are available for several pepper yellow leaf curl viruses, comparative evolutionary analyses across all recognized species remain limited. This study generated complete genome sequences for 3 PepYLCIV isolates using Oxford Nanopore sequencing and analyzed them together with publicly available genomes representing 4 recognized pepper yellow leaf curl virus species. The 3 isolates displayed the typical bipartite genome organization of PepYLCIV. Comparative genome analyses detected 14 recombination events in DNA-A and 9 in DNA-B, indicating that recombination has contributed substantially to genome diversification. Phylogenetic reconstruction and pairwise nucleotide identity analyses consistently placed the newly sequenced isolates within the PepYLCIV clade and resolved the 4 virus species as distinct evolutionary groups. Among the species examined, PepYLCIV showed the highest level of nucleotide diversity. Selection analyses indicated stronger purifying selection acting on DNA-A (ω = 0.049–0.111) than on DNA-B (ω = 0.768–0.839), consistent with the greater sequence variability of DNA-B. Population genetic analyses also revealed marked genetic differentiation among species (βFST = 0.765–0.991 for DNA-A and 0.751 for DNA-B). These findings expand the genomic resources available for PepYLCIV, provide new insights into the evolution of pepper yellow leaf curl viruses, and support future epidemiological surveillance, molecular detection, and resistance breeding in chili pepper.