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

The genus is agriculturally and ecologically important. As the number of 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 species. These genetic markers were the cytochrome- oxidase 1 (), internal transcribed spacer region (ITS), 60S ribosomal protein L10, beta-tubulin (β), elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA, and gene fusion protein (). As indicated by species distance, had the highest genus-wide resolution, followed by ITS, , and β. Resolution of these four markers also varied with (sub)clade. β alone could readily identify all species in clade 1, for clade 2, and 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 (96%) were easier to amplify than (75%) and (71%). Accordingly, it is recommended to take a two-step approach: classifying unknown 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.