Metatranscriptomic profiling uncovers a distinctive pepper virome in tropical Indonesia

Pepper (Capsicum annuum L.) is an important horticultural crop in Indonesia, yet the virome structure of pepper fields in the country remains largely unknown. Here, we used RNA-Seq-based metatranscriptomics to characterize viruses associated with symptomatic pepper plants from six geographically distinct locations in West Java. Six pooled regional libraries were analyzed, resulting in the identification of 129 plant virus-associated contigs. The pepper virome was strongly dominated by cucumber mosaic virus (CMV), while pepper vein yellows virus (PeVYV) and pepper yellow leaf curl Indonesia virus (PYLCIV) were consistently detected across all regions. Several lower-abundance viruses showed regional patterns, including chilli veinal mottle virus, potato virus Y, pepper cryptic virus 2, PeVYV-associated RNA, and tomato yellow leaf curl Kanchanaburi virus. Phylogenetic analyses suggested that CMV in West Java is related to an established Indonesian lineage, whereas PeVYV and PYLCIV populations are genetically structured across regions. In addition, RNA-Seq revealed two previously unrecognized putative virus-associated sequences related to tobacco bushy top virus and grapevine endophyte endornavirus. Because the libraries were generated from pooled samples, read-based values were interpreted as relative viral RNA abundance rather than field incidence. These findings reveal a CMV-dominated but regionally structured pepper virome in West Java and provide a foundation for virus surveillance and disease management in Indonesia.