{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T11:39:09Z","timestamp":1784893149188,"version":"3.55.0"},"reference-count":60,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T00:00:00Z","timestamp":1674086400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    Downy mildew is caused by\n                    <jats:italic>Plasmopara viticola<\/jats:italic>\n                    , an obligate oomycete plant pathogen, a devasting disease of grapevine. To protect plants from the disease, complex III inhibitors are among the fungicides widely used. They specifically target the mitochondrial cytochrome\n                    <jats:italic>b<\/jats:italic>\n                    (cyt\n                    <jats:italic>b<\/jats:italic>\n                    ) of the pathogen to block cellular respiration mechanisms. In the French vineyard,\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>viticola<\/jats:italic>\n                    has developed resistance against a first group of these fungicides, the Quinone outside Inhibitors (QoI), with a single amino acid substitution G143A in its cyt\n                    <jats:italic>b<\/jats:italic>\n                    mitochondrial sequence. The use of QoI was limited and another type of fungicide, the Quinone inside Inhibitors, targeting the same gene and highly effective against oomycetes, was used instead. Recently however, less sensitive\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>viticola<\/jats:italic>\n                    populations were detected after treatments with some inhibitors, in particular ametoctradin and cyazofamid. By isolating single-sporangia\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>viticola<\/jats:italic>\n                    strains resistant to these fungicides, we characterized new variants in the cyt\n                    <jats:italic>b<\/jats:italic>\n                    sequences associated with cyazofamid resistance: a point mutation (L201S) and more strikingly, two insertions (E203-DE-V204, E203-VE-V204). In parallel with the classical tools, pyrosequencing and qPCR, we then benchmarked short and long-reads NGS technologies (Ion Torrent, Illumina, Oxford Nanopore Technologies) to sequence the complete cyt\n                    <jats:italic>b<\/jats:italic>\n                    with a view to detecting and assessing the proportion of resistant variants of\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>viticola<\/jats:italic>\n                    at the scale of a field population. Eighteen populations collected from French vineyard fields in 2020 were analysed: 12 showed a variable proportion of G143A, 11 of E203-DE-V204 and 7 populations of the S34L variant that confers resistance to ametoctradin. Interestingly, the long reads were able to identify variants, including SNPs, with confidence and to detect a small proportion of\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>viticola<\/jats:italic>\n                    with multiple variants along the same cyt\n                    <jats:italic>b<\/jats:italic>\n                    sequence. Overall, NGS appears to be a promising method for assessing fungicide resistance of pathogens linked to cyt\n                    <jats:italic>b<\/jats:italic>\n                    modifications at the field population level. This approach could rapidly become a robust decision support tool for resistance management in the future.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0268385","type":"journal-article","created":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T13:35:06Z","timestamp":1674135306000},"page":"e0268385","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["New insights from short and long reads sequencing to explore cytochrome b variants in Plasmopara viticola populations collected from vineyards and related to resistance to complex III inhibitors"],"prefix":"10.1371","volume":"18","author":[{"given":"Semcheddine","family":"Cherrad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Gillet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien","family":"Dellinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lalie","family":"Bellaton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pascale","family":"Roux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catalina","family":"Hernandez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Herv\u00e9","family":"Steva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauriane","family":"Perrier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00e9bastien","family":"Vacher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3932-9180","authenticated-orcid":true,"given":"Sandrine","family":"Hughes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,1,19]]},"reference":[{"key":"pone.0268385.ref001","first-page":"10","article-title":"Colonization of Different Grapevine Tissues by Plasmopara viticola\u2014A Histological Study.","author":"S Fr\u00f6bel","year":"2019","journal-title":"Frontiers in Plant Science"},{"key":"pone.0268385.ref002","doi-asserted-by":"crossref","first-page":"382","DOI":"10.3389\/fpls.2016.00382","article-title":"Grapevine Pathogenic Microorganisms: Understanding Infection Strategies and Host Response Scenarios.","volume":"7","author":"G Armijo","year":"2016","journal-title":"Front Plant Sci"},{"key":"pone.0268385.ref003","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1111\/mpp.12190","article-title":"The Top 10 oomycete pathogens in molecular plant pathology","volume":"16","author":"S Kamoun","year":"2015","journal-title":"Molecular Plant Pathology"},{"key":"pone.0268385.ref004","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1094\/PHYTO-08-11-0223","article-title":"The Role of Rain in Dispersal of the Primary Inoculum of Plasmopara viticola","volume":"102","author":"V Rossi","year":"2012","journal-title":"Phytopathology\u00ae"},{"key":"pone.0268385.ref005","first-page":"3","article-title":"Plasmopara viticola: A review of knowledge on downy mildew of grapevine and effective disease management","volume":"50","author":"C Gessler","year":"2011","journal-title":"Phytopathologia Mediterranea"},{"key":"pone.0268385.ref006","first-page":"615","article-title":"Modelling the dynamics of infections caused by sexual and asexual spores during Plasmopara viticola epidemics","volume":"91","author":"V Rossi","year":"2009","journal-title":"Journal of Plant Pathology"},{"key":"pone.0268385.ref007","unstructured":"FRAC | Home. 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