Overestimation of Proteome Provides Insights into Transposable Element Landscape in Podosphaera xanthii, Causal Agent of Cucurbit Powdery Mildew Disease.

Abstract

Cucurbit powdery mildew, caused by Podosphaera xanthii, is one of the most destructive plant diseases of cucurbit crops worldwide. To date, there are discrepancies in the number of genes in the available genomic resources of the pathogen. We previously reported a predicted gene set of 16,030 in the P. xanthii isolate 2086, which was higher than that commonly described in other obligate biotrophic ascomycetes. The evaluation of the resulting proteome revealed approximately 7,000 consistent proteins and a surprising number of 8,940 unknown proteins. The study of this “dark” proteome showed that it actually originated from divergent transposable elements (TEs). For its part, the P. xanthii – Cucumis melo dual RNA-seq analysis showed a significant activity of some of these TEs during infection. Refining genome annotation taking into consideration repetitive elements could be critical for future metabolic and evolutionary studies aimed at understanding pathogen-host interactions.