{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T12:27:17Z","timestamp":1780316837945,"version":"3.54.1"},"reference-count":40,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2023,10,24]],"date-time":"2023-10-24T00:00:00Z","timestamp":1698105600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the SungKyunKwan University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>This study delves into the complex landscape of viral infections in tomatoes (Solanum lycopersicum) using available transcriptome data. We conducted a virome analysis, revealing 219 viral contigs linked to four distinct viruses: tomato chlorosis virus (ToCV), southern tomato virus (STV), tomato yellow leaf curl virus (TYLCV), and cucumber mosaic virus (CMV). Among these, ToCV predominated in contig count, followed by STV, TYLCV, and CMV. A notable finding was the prevalence of coinfections, emphasizing the concurrent presence of multiple viruses in tomato plants. Despite generally low viral levels in fruit transcriptomes, STV emerged as the primary virus based on viral read count. We delved deeper into viral abundance and the contributions of RNA segments to replication. While initially focused on studying the impact of sound treatment on tomato fruit transcriptomes, the unexpected viral presence underscores the importance of considering viruses in plant research. Geographical variations in virome communities hint at potential forensic applications. Phylogenetic analysis provided insights into viral origins and genetic diversity, enhancing our understanding of the Korean tomato virome. In conclusion, this study advances our knowledge of the tomato virome, stressing the need for robust pest control in greenhouse-grown tomatoes and offering insights into virus management and crop protection.<\/jats:p>","DOI":"10.3390\/v15112139","type":"journal-article","created":{"date-parts":[[2023,10,24]],"date-time":"2023-10-24T06:29:01Z","timestamp":1698128941000},"page":"2139","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Exploring Tomato Fruit Viromes through Transcriptome Data Analysis"],"prefix":"10.3390","volume":"15","author":[{"given":"Yeonhwa","family":"Jo","sequence":"first","affiliation":[{"name":"College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hoseong","family":"Choi","sequence":"additional","affiliation":[{"name":"Plant Health Center, Seoul National University, Seoul 08826, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bong Choon","family":"Lee","sequence":"additional","affiliation":[{"name":"Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin-Sung","family":"Hong","sequence":"additional","affiliation":[{"name":"Department of Applied Biology, Kangwon National University, Chuncheon 24341, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sang-Min","family":"Kim","sequence":"additional","affiliation":[{"name":"Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of 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, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,10,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/s11101-007-9085-x","article-title":"Tomato (Solanum lycopersicum) health components: From the seed to the consumer","volume":"7","author":"Dorais","year":"2008","journal-title":"Phytochem. Rev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"105086","DOI":"10.1016\/j.envexpbot.2022.105086","article-title":"Improving production and fruit quality of tomato under abiotic stress: Genes for the future of tomato breeding for a sustainable agriculture","volume":"204","author":"Egea","year":"2022","journal-title":"Environ. Exp. Bot."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1007\/s10681-015-1363-x","article-title":"Combined biotic and abiotic stress resistance in tomato","volume":"202","author":"Kissoudis","year":"2015","journal-title":"Euphytica"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.virol.2016.08.033","article-title":"Ongoing geographical spread of Tomato yellow leaf curl virus","volume":"498","author":"Mabvakure","year":"2016","journal-title":"Virology"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1221156","DOI":"10.3389\/fviro.2023.1221156","article-title":"Phylogenomic and population genetics analyses of extant tomato yellow leaf curl virus strains on a global scale","volume":"3","author":"Marchant","year":"2023","journal-title":"Front. Virol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/S0304-4238(96)00946-6","article-title":"Viral diseases causing the greatest economic losses to the tomato crop. I. The Tomato spotted wilt virus\u2014A review","volume":"67","author":"Nuez","year":"1996","journal-title":"Sci. Hortic."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1080\/14620316.2019.1691060","article-title":"Tomato yellow leaf curl virus disease of tomato and its management through resistance breeding: A review","volume":"95","author":"Dhaliwal","year":"2020","journal-title":"J. Hortic. Sci. Biotechnol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"83","DOI":"10.17221\/47\/2008-CJGPB","article-title":"Tomato breeding for resistance to Tomato spotted wilt virus (TSWV): An overview of conventional and molecular approaches","volume":"44","author":"Saidi","year":"2008","journal-title":"Czech J. Genet. Plant Breed."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1094\/PHYTO-07-18-0257-RVW","article-title":"High throughput sequencing for plant virus detection and discovery","volume":"109","author":"Villamor","year":"2019","journal-title":"Phytopathology"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Rivarez, M.P.S., Vu\u010durovi\u0107, A., Mehle, N., Ravnikar, M., and Kutnjak, D. (2021). Global advances in tomato virome research: Current status and the impact of high-throughput sequencing. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.671925"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e00173-17","DOI":"10.1128\/JVI.00173-17","article-title":"Diversity, distribution, and evolution of tomato viruses in China uncovered by small RNA sequencing","volume":"91","author":"Xu","year":"2017","journal-title":"J. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Rivarez, M.P.S., Pecman, A., Ba\u010dnik, K., Maksimovi\u0107, O., Vu\u010durovi\u0107, A., Seljak, G., Mehle, N., Guti\u00e9rrez-Aguirre, I., Ravnikar, M., and Kutnjak, D. (2023). In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem. Microbiome, 11.","DOI":"10.1186\/s40168-023-01500-6"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.virol.2019.11.009","article-title":"Metagenomic analysis of virome cross-talk between cultivated Solanum lycopersicum and wild Solanum nigrum","volume":"540","author":"Ma","year":"2020","journal-title":"Virology"},{"key":"ref_14","doi-asserted-by":"crossref","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":"ref_15","doi-asserted-by":"crossref","first-page":"193","DOI":"10.5423\/RPD.2017.23.2.193","article-title":"Specific primer sets for RT-PCR detection of major RNA viruses of tomato plants in Korea","volume":"23","author":"Shin","year":"2017","journal-title":"Res. Plant Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1007\/s11262-010-0541-0","article-title":"Genetic diversity of tomato-infecting Tomato yellow leaf curl virus (TYLCV) isolates in Korea","volume":"42","author":"Kim","year":"2011","journal-title":"Virus Genes"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1094\/PDIS-09-17-1499-PDN","article-title":"First report of Southern tomato virus in tomato (Solanum lycopersicum) in Korea","volume":"102","author":"Oh","year":"2018","journal-title":"Plant Dis."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"152","DOI":"10.5423\/PPJ.2008.24.2.152","article-title":"Isolation and characterization of Pepper mottle virus infecting tomato in Korea","volume":"24","author":"Kim","year":"2008","journal-title":"Plant Pathol. J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"143","DOI":"10.5423\/PPJ.2007.23.3.143","article-title":"First report on Tomato bushy stunt virus infecting tomato in Korea","volume":"23","author":"Kim","year":"2007","journal-title":"Plant Pathol. J."},{"key":"ref_20","first-page":"38","article-title":"Dual infections of Tomato mosaic virus (ToMV) and Tomato yellow leaf curl virus (TYLCV), or Tomato mosaic virus (ToMV) and Tomato chlorosis virus (ToCV), detected in tomato fields located in Chungcheongnam-do in 2017","volume":"45","author":"Choi","year":"2018","journal-title":"Korean J. Agric. Sci."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Choi, H., Jo, Y., Chung, H., Choi, S.Y., Kim, S.-M., Hong, J.-S., Lee, B.C., and Cho, W.K. (2023). Investigating Variability in Viral Presence and Abundance across Soybean Seed Development Stages Using Transcriptome Analysis. Plants, 12.","DOI":"10.3390\/plants12183257"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Choi, H., Jo, Y., and Cho, W.K. (2023). In Silico Virome Analysis of Chinese Narcissus Transcriptomes Reveals Diverse Virus Species and Genetic Diversity at Different Flower Development Stages. Biology, 12.","DOI":"10.3390\/biology12081094"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Jo, Y., Choi, H., Chu, H., and Cho, W.K. (2022). Unveiling Mycoviromes Using Fungal Transcriptomes. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms231810926"},{"key":"ref_24","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). Using RNA-sequencing data to examine tissue-specific garlic microbiomes. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22136791"},{"key":"ref_25","first-page":"1231","article-title":"Exploring the sound-modulated delay in tomato ripening through expression analysis of coding and non-coding RNAs","volume":"122","author":"Kim","year":"2018","journal-title":"Ann. Bot."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1038\/nprot.2013.084","article-title":"De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis","volume":"8","author":"Haas","year":"2013","journal-title":"Nat. Protoc."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1093\/bioinformatics\/btab754","article-title":"Mian: Interactive web-based microbiome data table visualization and machine learning platform","volume":"38","author":"Jin","year":"2022","journal-title":"Bioinformatics"},{"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":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"199","DOI":"10.5423\/PPJ.OA.10.2017.0220","article-title":"Phylogenetic characterization of Tomato chlorosis virus population in Korea: Evidence of reassortment between isolates from different origins","volume":"34","author":"Lee","year":"2018","journal-title":"Plant Pathol. J."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1094\/PHYTO-09-22-0334-R","article-title":"The crinivirus tomato chlorosis virus compromises the control of tomato yellow leaf curl virus in tomato plants by the Ty-1 gene","volume":"113","author":"Fortes","year":"2023","journal-title":"Phytopathology"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Kumar, M., Kavalappara, S.R., McAvoy, T., Hutton, S., Simmons, A.M., and Bag, S. (2023). Association of Tomato Chlorosis Virus Complicates the Management of Tomato Yellow Leaf Curl Virus in Cultivated Tomato (Solanum lycopersicum) in the Southern United States. Horticulturae, 9.","DOI":"10.3390\/horticulturae9080948"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Elvira Gonz\u00e1lez, L., Peir\u00f3, R., Rubio, L., and Galipienso, L. (2021). Persistent southern tomato virus (STV) interacts with cucumber mosaic and\/or pepino mosaic virus in mixed-infections modifying plant symptoms, viral titer and small RNA accumulation. Microorganisms, 9.","DOI":"10.3390\/microorganisms9040689"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1094\/PD-90-0814","article-title":"Vector specificity, host range, and genetic diversity of Tomato chlorosis virus","volume":"90","author":"Wintermantel","year":"2006","journal-title":"Plant Dis."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1016\/j.tplants.2020.03.015","article-title":"Tomato yellow leaf curl virus: Impact, challenges, and management","volume":"25","author":"Prasad","year":"2020","journal-title":"Trends Plant Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1111\/ppa.13771","article-title":"Detection of tomato brown rugose fruit virus is influenced by infection at different growth stages and sampling from different plant parts","volume":"72","author":"Skelton","year":"2023","journal-title":"Plant Pathol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.virusres.2008.11.018","article-title":"Southern tomato virus: The link between the families Totiviridae and Partitiviridae","volume":"140","author":"Sabanadzovic","year":"2009","journal-title":"Virus Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1111\/1556-4029.12065","article-title":"Legal, technical, and interpretational considerations in the forensic analysis of viruses","volume":"58","author":"Wilson","year":"2013","journal-title":"J. Forensic Sci."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/11\/2139\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T21:10:51Z","timestamp":1760130651000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/11\/2139"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,24]]},"references-count":40,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2023,11]]}},"alternative-id":["v15112139"],"URL":"https:\/\/doi.org\/10.3390\/v15112139","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,24]]}}}