{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T06:15:33Z","timestamp":1788156933000,"version":"build-2803163510"},"reference-count":30,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    High-throughput sequencing (HTS) can support plant virus surveillance, but host nucleic acids often reduce on-target read recovery. We evaluated a targeted hybridization-capture workflow in which barcoded double-stranded cDNA (ds-cDNA) libraries generated from plant RNA extracts spiked with lyophilized tobamovirus-positive controls were enriched before Oxford Nanopore sequencing. Biotinylated probes targeted conserved regions of cucumber green mottle mosaic virus (CGMMV), species\n                    <jats:italic>Tobamovirus viridimaculae<\/jats:italic>\n                    ; pepper mild mottle virus (PMMoV), species\n                    <jats:italic>Tobamovirus capsici<\/jats:italic>\n                    ; and tobacco mosaic virus (TMV), species\n                    <jats:italic>Tobamovirus tabaci<\/jats:italic>\n                    . Across four pairs per virus, relative target-read abundance increased after capture from 0.76 \u00b1 0.33% to 37.62 \u00b1 15.72% for CGMMV, 8.16 \u00b1 3.86% to 24.68 \u00b1 12.34% for PMMoV, and 15.62 \u00b1 10.40% to 36.83 \u00b1 30.33% for TMV. Exact two-sided Wilcoxon signed-rank tests yielded\n                    <jats:italic>P<\/jats:italic>\n                    = 0.125 for each virus; with four nonzero differences in a common direction, this was the minimum attainable two-sided\n                    <jats:italic>P<\/jats:italic>\n                    value. Genome-coverage breadth was maintained. Retrospective duplex qPCR supported an increased virus-to-18S ratio for CGMMV, showed a variable PMMoV response, and showed a decreased virus-to-18S ratio for TMV because the 18S signal shifted earlier by as much as or more than the TMV signal. The findings provide proof-of-concept evidence for target-dependent library enrichment but do not establish analytical sensitivity, diagnostic performance, or field validity. Validation with naturally infected, low-titer, and mixed-infection samples and comparison with simpler targeted workflows are required.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1925769","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T05:39:33Z","timestamp":1788154773000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Hybridization capture increases on-target nanopore sequencing of plant RNA tobamovirus- derived cDNA libraries"],"prefix":"10.3389","volume":"17","author":[{"given":"Andres S.","family":"Espindola","sequence":"first","affiliation":[{"name":"Institute for Biosecurity and Microbial Forensics, Oklahoma State University","place":["Stillwater, OK, United States"]},{"name":"Department of Entomology and Plant Pathology, Oklahoma State University","place":["Stillwater, OK, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco","family":"Mosquera-Yuqui","sequence":"additional","affiliation":[{"name":"Institute for Biosecurity and Microbial Forensics, Oklahoma State University","place":["Stillwater, OK, United States"]},{"name":"Department of Entomology and Plant Pathology, Oklahoma State University","place":["Stillwater, OK, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco","family":"Ochoa-Corona","sequence":"additional","affiliation":[{"name":"Institute for Biosecurity and Microbial Forensics, Oklahoma State University","place":["Stillwater, OK, United States"]},{"name":"Department of Entomology and Plant Pathology, Oklahoma State University","place":["Stillwater, OK, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Marek","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, Oklahoma State University","place":["Stillwater, OK, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"B1","first-page":"5","article-title":"Mosaic diseases of the cucumber","volume-title":"The Annals of Applied Biology","author":"Ainsworth","year":"1935"},{"key":"B2","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1111\/j.1364-3703.2009.00537.x","article-title":"Microbe-associated molecular pattern (MAMP) signatures, synergy, size and charge: Influences on perception or mobility and host defence responses.","volume":"10","author":"Aslam","year":"2009","journal-title":"Mol. 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