Differential Usefulness of Nine Commonly Used Genetic Markers for Identifying Phytophthora Species

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dc.contributor.authorYang, Xiaoen
dc.contributor.authorHong, Chuanxueen
dc.contributor.departmentVirginia Agricultural Experiment Stationen
dc.date.accessioned2019-01-18T19:04:14Zen
dc.date.available2019-01-18T19:04:14Zen
dc.date.issued2018-10-03en
dc.description.abstractThe genus Phytophthora is agriculturally and ecologically important. As the number of Phytophthora species continues to grow, identifying isolates in this genus has become increasingly challenging even by DNA sequencing. This study evaluated nine commonly used genetic markers against 154 formally described and 17 provisionally named Phytophthora species. These genetic markers were the cytochrome-c oxidase 1 (cox1), internal transcribed spacer region (ITS), 60S ribosomal protein L10, beta-tubulin (-tub), elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA, and tigA gene fusion protein (tigA). As indicated by species distance, cox1 had the highest genus-wide resolution, followed by ITS, tigA, and -tub. Resolution of these four markers also varied with (sub)clade. -tub alone could readily identify all species in clade 1, cox1 for clade 2, and tigA for clades 7 and 8. Two or more genetic markers were required to identify species in other clades. For PCR consistency, ITS (99% PCR success rate) and -tub (96%) were easier to amplify than cox1 (75%) and tigA (71%). Accordingly, it is recommended to take a two-step approach: classifying unknown Phytophthora isolates to clade by ITS sequences, as this marker is easy to amplify and its signature sequences are readily available, then identifying to species by one or more of the most informative markers for the respective (sub)clade.en
dc.description.sponsorshipThis research was supported in part by grants from the USDANIFA- Specialty Crop Research Initiative (Agreement no. 2010- 51181-21140). The authors would like to thank Mrs. Patricia Richardson for her assistance in submitting PCR products for DNA sequencing during the study and her proofreading of this manuscript. We thank Virginia Tech’s Open Access Subvention Fund (OASF) for financial support of publication fees.en
dc.description.sponsorshipUSDA-NIFA-Specialty Crop Research Initiative (Agreement no. 2010- 51181-21140)en
dc.format.extent14 pagesen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationYang X and Hong C (2018) Differential Usefulness of Nine Commonly Used Genetic Markers for Identifying Phytophthora Species. Front. Microbiol. 9:2334. doi: 10.3389/fmicb.2018.02334en
dc.identifier.doihttps://doi.org/10.3389/fmicb.2018.02334en
dc.identifier.urihttp://hdl.handle.net/10919/86767en
dc.identifier.volume9en
dc.language.isoenen
dc.publisherFrontiersen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectoomycetesen
dc.subjectplant disease diagnosisen
dc.subjectplant pathologyen
dc.subjectgeneticsen
dc.subjectplant destroyersen
dc.titleDifferential Usefulness of Nine Commonly Used Genetic Markers for Identifying Phytophthora Speciesen
dc.title.serialFrontiers in Microbiologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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