Phytophthora capsici carries and differentially expresses genes that encode key enzymes for the synthesis, transport and processing of small RNAs

The small RNA (sRNA) pathway is an epigenetic mechanism that has recently gained attention due to its suggested role in regulating virulence of plant pathogens. This gene silencing process has been observed in certain species of the oomycete genus Phytophthora. However, little is known about this pathway in Phytophthora capsici, a pathogen with a broad host range that affects many important food crops. In the present study, using bioinformatics approaches on the reference genome, transcriptome, and proteome of P. capsici, we identified and analyzed key genes and proteins involved in the synthesis, transport, and processing of sRNAs. Our results showed that the P. capsici genome encodes a DCL, DCL{beta}, exportin-5A, RDR, and six AGO proteins, suggesting the presence of a complete sRNA pathway in this pathogen. These genes were syntenic, structurally similar, and phylogenetically related to other oomycetes of the genus Phytophthora. We also analyzed their expression levels after infecting chili pepper and broccoli across two generations, revealing different expression patterns depending on the pathogen infection history. To our knowledge, this is the first report showing the presence of the exportin-5A gene in P. capsici and other oomycetes. Additionally, the expression of all these sRNA-related genes in the pathogen isolated from different hosts suggests that the host may influence the epigenetic regulation of P. capsici via the sRNA pathway. This study paves the way for functional studies to confirm the role of the sRNA pathway in regulating virulence in P. capsici.