{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T06:12:24Z","timestamp":1788502344919,"version":"build-2803163510"},"reference-count":28,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T00:00:00Z","timestamp":1788480000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003627","name":"Rural Development Administration","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003627","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    Pepper (\n                    <jats:italic>Capsicum annuum<\/jats:italic>\n                    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.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1933649","type":"journal-article","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T05:28:40Z","timestamp":1788499720000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Metatranscriptomic profiling uncovers a distinctive pepper virome in tropical Indonesia"],"prefix":"10.3389","volume":"17","author":[{"given":"Andika Septiana","family":"Suryaningsih","sequence":"first","affiliation":[{"name":"Department of International Agricultural Technology, Seoul National University","place":["Pyeongchang, Republic of Korea"]},{"name":"Department of Plant Protection, Faculty of Agriculture, IPB University","place":["Bogor, Indonesia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seok-Yeong","family":"Jang","sequence":"additional","affiliation":[{"name":"Department of International Agricultural Technology, Seoul National University","place":["Pyeongchang, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhayanti","family":"Makyorukty","sequence":"additional","affiliation":[{"name":"Department of International Agricultural Technology, Seoul National University","place":["Pyeongchang, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hee-Seong","family":"Byun","sequence":"additional","affiliation":[{"name":"Crop Protection Division, National Institute of Agricultural Sciences","place":["Rural Development Administration, Wanju, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wahyu Ridwan","family":"Nanta","sequence":"additional","affiliation":[{"name":"People\u2019s Coalition for Food Sovereignty","place":["Bogor, West Java, Indonesia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Won Kyong","family":"Cho","sequence":"additional","affiliation":[{"name":"Agriculture and Life Sciences Research Institute, Kangwon National University","place":["Chuncheon, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sun-Jung","family":"Kwon","sequence":"additional","affiliation":[{"name":"Institutes of Green Bio Science and Technology, Seoul National University","place":["Pyeongchang, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jang-Kyun","family":"Seo","sequence":"additional","affiliation":[{"name":"Department of International Agricultural Technology, Seoul National University","place":["Pyeongchang, Republic of Korea"]},{"name":"Institutes of Green Bio Science and Technology, Seoul National University","place":["Pyeongchang, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,4]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3390\/v15122402","article-title":"Novel tri-segmented rhabdoviruses: A data mining expedition unveils the cryptic diversity of cytorhabdoviruses","volume":"15","author":"Bejerman","year":"2023","journal-title":"Viruses"},{"key":"B2","first-page":"23","article-title":"Mosaic disease and chilli production on different altitudes in South Sumatra, Indonesia","volume":"47","author":"Damiri","year":"2018","journal-title":"Malays. Appl. Biol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1094\/php-10-22-0107-rs","article-title":"Viromes of field-grown tomatoes and peppers in Tennessee revealed by RNA sequencing followed by bioinformatic analysis","volume":"24","author":"Dias","year":"2023","journal-title":"Plant Health Prog."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2020.104132","article-title":"The threat of seed-transmissible pepper yellow leaf curl Indonesia virus in chili pepper","volume":"143","author":"Fadhila","year":"2020","journal-title":"Microb. Pathog."},{"key":"B5","doi-asserted-by":"publisher","first-page":"590614","DOI":"10.34044\/j.anres.2025.59.6.14","article-title":"Characterization of Begomovirus and Potyvirus causing mixed infections on chili plant (Capsicum frutescens L.) in South Lampung, Indonesia","volume":"59","author":"Helina","year":"2025","journal-title":"Agr. Nat. Resour."},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veaa070","article-title":"Newly emerged resistance-breaking variants of cucumber mosaic virus represent ongoing host-interactive evolution of an RNA virus","volume":"6","author":"Heo","year":"2020","journal-title":"Virus Evol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1186\/s12864-017-3838-8","article-title":"The pepper virome: Natural co-infection of diverse viruses and their quasispecies","volume":"18","author":"Jo","year":"2017","journal-title":"BMC Genomics"},{"key":"B8","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1094\/phyto-10-13-0275-r","article-title":"Molecular genetic analysis of cucumber mosaic virus populations infecting pepper suggests unique patterns of evolution in Korea","volume":"104","author":"Kim","year":"2014","journal-title":"Phytopathology"},{"key":"B9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1101\/2024.12.10.627672","article-title":"MEGA12: Molecular evolutionary genetic analysis version 12 for adaptive and green computing","volume":"41","author":"Kumar","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"7261","DOI":"10.1038\/s41598-023-34553-6","article-title":"Visual tracking of viral infection dynamics reveals the synergistic interactions between cucumber mosaic virus and broad bean wilt virus 2","volume":"13","author":"Kwon","year":"2023","journal-title":"Sci. Rep."},{"key":"B11","doi-asserted-by":"publisher","first-page":"66","DOI":"10.5423\/rpd.2018.24.1.66","article-title":"Incidence and occurrence pattern of viruses on peppers growing in fields in Korea","volume":"24","author":"Kwon","year":"2018","journal-title":"Res. Plant Dis."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcp.2022.101792","article-title":"A multiplex RT-PCR assay for detection of emergent pepper Tsw resistance-breaking variants of tomato spotted wilt virus in South Korea","volume":"61","author":"Kwon","year":"2022","journal-title":"Mol. Cell. Probes"},{"key":"B13","doi-asserted-by":"publisher","first-page":"2771","DOI":"10.1094\/pdis-01-21-0205-sc","article-title":"Resistance-breaking tomato spotted wilt virus variant that recently occurred in pepper in South Korea is a genetic reassortant","volume":"105","author":"Kwon","year":"2021","journal-title":"Plant Dis."},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.623875","article-title":"A multiyear survey and identification of pepper- and tomato-infecting viruses in Yunnan Province, China","volume":"12","author":"Li","year":"2021","journal-title":"Front. Microbiol."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0063380","article-title":"Phylogenetic and recombination analysis of tomato spotted wilt virus","volume":"8","author":"Lian","year":"2013","journal-title":"PloS One"},{"key":"B16","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1094\/phyto-96-0240","article-title":"Synergistic disease in pepper caused by the mixed infection of cucumber mosaic virus and pepper mottle virus","volume":"96","author":"Murphy","year":"2006","journal-title":"Phytopathology"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0221834","article-title":"Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses","volume":"15","author":"Rumbou","year":"2020","journal-title":"PloS One"},{"key":"B18","unstructured":"Genus umbravirus virus taxonomy: ninth report of the international committee on taxonomy of viruses\n          \n          \n            \n              Ryabov\n              E.\n            \n            \n              Talianksy\n              M.\n            \n            \n              Robinson\n              D. G.\n            \n            \n              Waterhouse\n              P. M.\n            \n            \n              Zoeten\n              G. A.\n            \n            \n              Falk\n              B. W.\n            \n          \n          Virus Taxonomy\n          \n          2012"},{"key":"B19","doi-asserted-by":"publisher","first-page":"120","DOI":"10.20956\/ijas.v5i2.1201","article-title":"Impact of red chilli reference price policy in Indonesia","volume":"5","author":"Sativa","year":"2017","journal-title":"Int. J. Agr. Syst."},{"key":"B20","doi-asserted-by":"publisher","first-page":"2885","DOI":"10.1007\/s00705-017-3405-2","article-title":"Complete genome sequence of longan witches' broom-associated virus, a novel member of the family Potyviridae","volume":"162","author":"Seo","year":"2017","journal-title":"Arch. Virol."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.01232","article-title":"Robust virome profiling and whole genome reconstruction of viruses and viroids enabled by use of available mRNA and sRNA-Seq datasets in grapevine (Vitis vinifera L.)","volume":"11","author":"Sidharthan","year":"2020","journal-title":"Front. Microbiol."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3389\/fbinf.2022.867111","article-title":"VirHunter: A deep learning-based method for detection of novel RNA viruses in plant sequencing data","volume":"2","author":"Sukhorukov","year":"2022","journal-title":"Front. Bioinform."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1016\/j.microb.2026.100724","article-title":"Cucumber mosaic virus variant with divergent RNA2 infecting solanaceous crops and their weeds in Java Island, Indonesia","volume":"11","author":"Surwadinata","year":"2026","journal-title":"Microbe"},{"key":"B24","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1094\/pdis-08-25-1726-pdn","article-title":"First report of pepper cryptic virus 2 in chili pepper in Indonesia","volume":"110","author":"Suryaningsih","year":"2026","journal-title":"Plant Dis."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1099\/jgv.0.001277","article-title":"ICTV virus taxonomy profile: Endornaviridae","volume":"100","author":"Valverde","year":"2019","journal-title":"J. Gen. Virol."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.3390\/v15061278","article-title":"Current status and complexity of three begomovirus species in pepper plants in lowlands and highlands in Java Island, Indonesia","volume":"15","author":"Wahyono","year":"2023","journal-title":"Viruses"},{"key":"B27","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/j.atmosres.2016.03.017","article-title":"Physical climatology of Indonesian maritime continent: An outline to comprehend observational studies","volume":"178","author":"Yamanaka","year":"2016","journal-title":"Atmos. Res."},{"key":"B28","doi-asserted-by":"publisher","first-page":"68","DOI":"10.22146\/jpti.88503","article-title":"Population of Bemisia tabaci and incidence of yellow disease in chili intercropped with corn","volume":"28","author":"Yolanda","year":"2024","journal-title":"Indones. J. Plant Prot."}],"container-title":["Frontiers in Plant Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1933649\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T05:28:42Z","timestamp":1788499722000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1933649\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,4]]},"references-count":28,"alternative-id":["10.3389\/fpls.2026.1933649"],"URL":"https:\/\/doi.org\/10.3389\/fpls.2026.1933649","relation":{},"ISSN":["1664-462X"],"issn-type":[{"value":"1664-462X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,4]]},"article-number":"1933649"}}