{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:24:20Z","timestamp":1791386660409,"version":"4.3.3"},"reference-count":32,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2022,9,10]],"date-time":"2022-09-10T00:00:00Z","timestamp":1662768000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET)","award":["121054-2"],"award-info":[{"award-number":["121054-2"]}]},{"name":"Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET)","award":["NRF-2018R1D1A1B07043597"],"award-info":[{"award-number":["NRF-2018R1D1A1B07043597"]}]},{"DOI":"10.13039\/501100003668","name":"Ministry of Agriculture, Food, and Rural Affairs (MAFRA)","doi-asserted-by":"publisher","award":["121054-2"],"award-info":[{"award-number":["121054-2"]}],"id":[{"id":"10.13039\/501100003668","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003668","name":"Ministry of Agriculture, Food, and Rural Affairs (MAFRA)","doi-asserted-by":"publisher","award":["NRF-2018R1D1A1B07043597"],"award-info":[{"award-number":["NRF-2018R1D1A1B07043597"]}],"id":[{"id":"10.13039\/501100003668","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Research Foundation of Korea (NRF)","award":["121054-2"],"award-info":[{"award-number":["121054-2"]}]},{"name":"National Research Foundation of Korea (NRF)","award":["NRF-2018R1D1A1B07043597"],"award-info":[{"award-number":["NRF-2018R1D1A1B07043597"]}]},{"name":"Korea government (MSIT)","award":["121054-2"],"award-info":[{"award-number":["121054-2"]}]},{"name":"Korea government (MSIT)","award":["NRF-2018R1D1A1B07043597"],"award-info":[{"award-number":["NRF-2018R1D1A1B07043597"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Pepper (Capsicum annuum L.) plants produce berry fruits that are used as spices. Here, we examined the viromes of 15 pepper cultivars through RNA sequencing. We obtained 1,325 virus-associated contigs derived from 8 virus species. Bean broad wilt virus 2 (BBWV2) and cucumber mosaic virus (CMV) were identified as the major viruses infecting pepper plants, followed by potato virus Y, bell pepper endornavirus, and hot pepper endornavirus. The proportion of viral reads in each transcriptome ranged from 0.04% to 24.5%. BBWV2 was the dominant virus in seven cultivars, whereas CMV was dominant in five cultivars. All the bell pepper cultivars showed severe viral disease symptoms, whereas the commercially developed hot pepper cultivars were asymptomatic or had mild symptoms. In addition, 111 complete viral segments were obtained from 7 viruses. Based on the obtained viral genomes, the genetic relationship between the identified viruses and quasispecies of BBWV2 and CMV in each pepper plant was determined. Newly designed primers for nine viruses confirmed the results of RNA sequencing. Taken together, this study, for the first time, provides a comprehensive overview of viromes in 15 major pepper cultivars through RNA sequencing.<\/jats:p>","DOI":"10.3390\/ijms231810507","type":"journal-article","created":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T22:53:46Z","timestamp":1663023226000},"page":"10507","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Viromes of 15 Pepper (Capsicum annuum L.) Cultivars"],"prefix":"10.3390","volume":"23","author":[{"given":"Yeonhwa","family":"Jo","sequence":"first","affiliation":[{"name":"College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hoseong","family":"Choi","sequence":"additional","affiliation":[{"name":"Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeong Hun","family":"Lee","sequence":"additional","affiliation":[{"name":"Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2175-7224","authenticated-orcid":false,"given":"Sang Hyun","family":"Moh","sequence":"additional","affiliation":[{"name":"Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8416-5173","authenticated-orcid":false,"given":"Won Kyong","family":"Cho","sequence":"additional","affiliation":[{"name":"College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,10]]},"reference":[{"key":"ref_1","unstructured":"Basu, S.K., and De, A.K. (2003). Capsicum: Historical and botanical perspectives. Capsicum, CRC Press."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2239","DOI":"10.1002\/fsn3.790","article-title":"The suitability of chili pepper (Capsicum annuum L.) for alleviating human micronutrient dietary deficiencies: A review","volume":"6","author":"Olatunji","year":"2018","journal-title":"Food Sci. Nutr."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"6165","DOI":"10.1073\/pnas.1308933111","article-title":"Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico","volume":"111","author":"Kraft","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.jef.2014.11.003","article-title":"History of Korean gochu, gochujang, and kimchi","volume":"1","author":"Kwon","year":"2014","journal-title":"J. Ethn. Foods"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Jo, Y., Choi, H., Kim, S.-M., Kim, S.-L., Lee, B.C., and Cho, W.K. (2017). The pepper virome: Natural co-infection of diverse viruses and their quasispecies. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3838-8"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Choi, H., Jo, Y., Cho, W.K., Yu, J., Tran, P.-T., Salaipeth, L., Kwak, H.-R., Choi, H.-S., and Kim, K.-H. (2020). Identification of viruses and viroids infecting tomato and pepper plants in vietnam by metatranscriptomics. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21207565"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"258","DOI":"10.5423\/PPJ.2005.21.3.258","article-title":"Occurrence and distribution of viruses infecting pepper in Korea","volume":"21","author":"Choi","year":"2005","journal-title":"Plant Pathol. J."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Jo, Y., Back, C.-G., Kim, K.-H., Chu, H., Lee, J.H., Moh, S.H., and Cho, W.K. (2021). Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22126202"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.virol.2017.03.018","article-title":"Phylogenetic study of recombinant strains of Potato virus Y","volume":"507","author":"Green","year":"2017","journal-title":"Virology"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Glasa, M., Han\u010dinsk\u00fd, R., \u0160oltys, K., Predaj\u0148a, L., Toma\u0161echov\u00e1, J., Hauptvogel, P., Mrkvov\u00e1, M., Mih\u00e1lik, D., and Candresse, T. (2021). Molecular characterization of Potato Virus Y (PVY) using high-throughput sequencing: Constraints on full genome reconstructions imposed by mixed infection involving recombinant PVY strains. Plants, 10.","DOI":"10.3390\/plants10040753"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Mrkvov\u00e1, M., Han\u010dinsk\u00fd, R., Predaj\u0148a, L., Alaxin, P., Achs, A., Toma\u0161echov\u00e1, J., \u0160oltys, K., Mih\u00e1lik, D., Olmos, A., and Ruiz-Garc\u00eda, A.B. (2022). High-Throughput Sequencing Discloses the Cucumber Mosaic Virus (CMV) Diversity in Slovakia and Reveals New Hosts of CMV from the Papaveraceae Family. Plants, 11.","DOI":"10.3390\/plants11131665"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2439","DOI":"10.1093\/jxb\/erw069","article-title":"Pepper CabZIP63 acts as a positive regulator during Ralstonia solanacearum or high temperature\u2013high humidity challenge in a positive feedback loop with CaWRKY40","volume":"67","author":"Shen","year":"2016","journal-title":"J. Exp. Bot."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"274","DOI":"10.5423\/PPJ.OA.12.2012.0190","article-title":"Genetic compositions of Broad bean wilt virus 2 infecting red pepper in Korea","volume":"29","author":"Kwak","year":"2013","journal-title":"Plant Pathol. J."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1094\/PDIS-03-13-0232-PDN","article-title":"First Report of Broad bean wilt virus-2 in Pepper in the Czech Republic","volume":"97","author":"Svoboda","year":"2013","journal-title":"Plant Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"3153","DOI":"10.1007\/s00705-015-2616-7","article-title":"Complete genome sequence of a novel endornavirus isolated from hot pepper","volume":"160","author":"Lim","year":"2015","journal-title":"Arch. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1007\/s42161-019-00366-8","article-title":"First report of hot pepper endornavirus infecting pepper in China","volume":"102","author":"Zhang","year":"2020","journal-title":"J. Plant Pathol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1016\/j.gene.2015.09.051","article-title":"In silico identification of Bell pepper endornavirus from pepper transcriptomes and their phylogenetic and recombination analyses","volume":"575","author":"Jo","year":"2016","journal-title":"Gene"},{"key":"ref_18","doi-asserted-by":"crossref","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":"ref_19","doi-asserted-by":"crossref","first-page":"349","DOI":"10.5423\/PPJ.2005.21.4.349","article-title":"Characteristics of Potato virus Y isolated from paprika in Korea","volume":"21","author":"Choi","year":"2005","journal-title":"Plant Pathol. J."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1016\/j.jviromet.2009.09.026","article-title":"Seed transmission of Cucumber mosaic virus in pepper","volume":"163","author":"Ali","year":"2010","journal-title":"J. Virol. Methods"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.virol.2015.03.022","article-title":"Viral quasispecies","volume":"479\u2013480","author":"Andino","year":"2015","journal-title":"Virology"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"210","DOI":"10.5423\/PPJ.2003.19.4.210","article-title":"A Subpopulation of RNA3 of Cucumber mosaic virus Quasispecies","volume":"19","author":"Park","year":"2003","journal-title":"Plant Pathol. J."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"6566","DOI":"10.1128\/JVI.75.14.6566-6571.2001","article-title":"Genetic diversity in RNA virus quasispecies is controlled by host-virus interactions","volume":"75","author":"Schneider","year":"2001","journal-title":"J. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"598798","DOI":"10.3389\/fpls.2020.598798","article-title":"Pepper crop improvement against cucumber mosaic virus (CMV): A review","volume":"11","author":"Li","year":"2020","journal-title":"Front. Plant Sci."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Huson, D.H., Beier, S., Flade, I., G\u00f3rska, A., El-Hadidi, M., Mitra, S., Ruscheweyh, H.-J., and Tappu, R. (2016). MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol., 12.","DOI":"10.1371\/journal.pcbi.1004957"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1093\/nar\/28.1.10","article-title":"Database resources of the national center for biotechnology information","volume":"28","author":"Wheeler","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: Improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1093\/bioinformatics\/bty701","article-title":"PrimedRPA: Primer design for recombinase polymerase amplification assays","volume":"35","author":"Higgins","year":"2019","journal-title":"Bioinformatics"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/18\/10507\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:29:05Z","timestamp":1760142545000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/18\/10507"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,10]]},"references-count":32,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2022,9]]}},"alternative-id":["ijms231810507"],"URL":"https:\/\/doi.org\/10.3390\/ijms231810507","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,10]]}}}