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Title: Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach

item CHOI, YOUNG-JOON - Biodiversity And Climate Research Centre (BIK-F)
item Klosterman, Steven
item KUMMER, VOLKER - Potsdam Institute
item VOGLMAYR, HERMANN - University Of Vienna
item SHIN, HYEON-DONG - Korea University
item THINES, MARCO - Biodiversity And Climate Research Centre (BIK-F)

Submitted to: Molecular Phylogenetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2015
Publication Date: 3/12/2015
Citation: Choi, Y.-J., Klosterman, S.J., Kummer, V., Voglmayr, H., Shin, H.-D., Thines, M. 2015. Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach. Molecular Phylogenetics and Evolution. 86:24–34.

Interpretive Summary: Classification of plant pathogens into the appropriate species designations is important for appropriate diagnosis to control the diseases caused by these pathogens. Many Downy mildew pathogens in the genus Peronospora are currently being reclassified. The species designation of Peronospora farinosa has long been used to denote the causal agents of multiple downy mildew diseases, on different plant hosts. However, the downy mildew pathogens have very narrow host ranges; the spinach downy mildew pathogen only infects spinach and the closely related beet downy mildew pathogen only infects beet plants. In this study, DNA sequence evidence was used to distinguish the downy mildew pathogens of beet, spinach, and related fungus-like organisms as distinct species. Based upon the evidence presented, the previous species designation of Peronospora schachtii, which causes downy mildew on beet, is reconsidered as the most appropriate for this distinct species.

Technical Abstract: Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants.