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Front. Microbiol. | doi: 10.3389/fmicb.2018.02334

Differential usefulness of nine commonly used genetic markers for identifying Phytophthora species

  • 1Virginia Tech, United States

The genus Phytophthora is agriculturally and ecologically important. As the number of described 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 (β-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 β-tub. Resolution of these four markers also varied with (sub)clade. β-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 β-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.

Keywords: Oomycetes, Plant disease diagnosis, Plant Pathology, Genetics, Phytopathology

Received: 03 Aug 2018; Accepted: 12 Sep 2018.

Edited by:

Hector Mora Montes, Universidad de Guanajuato, Mexico

Reviewed by:

Henrik R. Nilsson, University of Gothenburg, Sweden
Bernardo Franco, Universidad de Guanajuato, Mexico  

Copyright: © 2018 Yang and Hong. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Xiao Yang, Virginia Tech, Blacksburg, United States, yxiao9@vt.edu