‘Jumping Jack’: Genomic microsatellites underscore the distinctiveness of closely related Pseudoperonospora cubensis and Pseudoperonospora humuli and provide new insights into their evolutionary past

Authors: NOWICKI, MARCIN - University Of Tennessee; HADZIABDIC-GUERRY, DENITA - University Of Tennessee; TRIGIANO, ROBERT - University Of Tennessee; BOGGESS, SARAH - University Of Tennessee; KANETIS, LOUKAS - Cyprus University Of Technology; Wadl, Phillip; OJIAMBO, PETER - North Carolina State University; CUBETA, MARC - North Carolina State University; SPRING, OTMAR - Goethe University; THINES, MARCO - University Of Hohenheim; RUNGE, FABIEN - Idexx Laboratories; Scheffler, Brian

Submitted to: Molecular Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/2/2021
Publication Date: 7/14/2021
Citation: Nowicki, M., Hadziabdic-Guerry, D., Trigiano, R.N., Boggess, S.L., Kanetis, L., Wadl, P.A., Ojiambo, P.S., Cubeta, M.A., Spring, O., Thines, M., Runge, F., Scheffler, B.E. 2021. ‘Jumping Jack’: Genomic microsatellites underscore the distinctiveness of closely related Pseudoperonospora cubensis and Pseudoperonospora humuli and provide new insights into their evolutionary past. Molecular Plant Pathology. 12:686759. https://doi.org/10.3389/fmicb.2021.686759.
DOI: https://doi.org/10.3389/fmicb.2021.686759

Interpretive Summary: Downy mildews are plant pathogens that require living host tissue to grow and reproduce. Two of these pathogens, Pseudoperonospora cubensis and P. humuli cause considerable economic losses of cucurbits (cucumber, melon, squash, and watermelon) and hops through crop loss and costs associated with crop protection. The taxonomic descriptions of these pathogen species have been revised several times based on the emerging phytopathological, epidemiological, and molecular evidence. Several studies have discussed the critical need for a comparative molecular population-genetics approach to investigate and help determine if the two species are distinct. Extensive comparative population genetics research is lacking for the two species. Therefore, an international team that included ARS scientists used microsatellite markers (SSRs) to assess genetic diversity and spatial distribution, to infer evolutionary history of P. cubensis and P. humuli, and to visualize genome-scale organizational relationship between both pathogens. The study found high genetic diversity, modest gene flow, and presence of population structure, particularly in P. cubensis. In summary, our population genetics study on the taxonomic identity of closely related downy mildew pathogens P. cubensis and P. humuli using SSRs provided the definite proof for the separation of both species. The data accrued allowed novel insights into the evolutionary history, reliably separating the P. cubensis samples from cucumber from those of other cucurbits, as well as P. humuli from hop. Lastly, leveraging the ability of SSRs to differentiate and host information allows replacement of the current resource-intensive bioassay based pathotyping of P. cubensis isolates.

Technical Abstract: Downy mildews caused by obligate oomycetes result in severe crop losses worldwide. Among these pathogens, Pseudoperonospora cubensis and P. humuli, two closely related species, adversely affect cucurbits and hops, respectively. Discordant hypotheses concerning their taxonomic relationships have been proposed based on phytopathological evidence and gene sequences of few individuals, but population genetics evidence for this taxonomic claim is missing. Further, nuclear and mitochondrial regions of both pathogens have been analyzed using microsatellites and other molecular methods, but extensive comparative population genetics research is still lacking. Here, we genotyped 129 current and historical herbarium specimens of the two species using microsatellites (SSRs). Our goals were to assess genetic diversity and spatial distribution, to infer evolutionary history of P. cubensis and P. humuli, and to visualize genome-scale organizational relationship between both pathogens. High genetic diversity, modest gene flow, and presence of population structure, particularly in P. cubensis were indicated. When tested for cross-amplification, 20 out of 27 of P. cubensis-derived SSRs cross-amplified DNA of P. humuli individuals, but only few produced amplification products with downy mildews from related genera. Comparative genomics analyses of the available draft genome sequences evidenced synteny at both the genomic DNA and the translated sequence levels, with tandem repeats expansion in the P. humuli genome. Collectively, our analyses provided a definite argument for the hypothesis that both pathogens are distinct species.