Rojas-Rojas, F. U. | bioRxiv Science

bioRxiv2025

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.

molecular biology↗

bioRxiv2025

Host-Specific Transcriptional Responses of Phytophthora capsici During Early Crown Infection in Cucurbitaceous and Solanaceous Plants

Phytophthora capsici is a destructive, broad-host-range oomycete responsible for substantial losses in global agriculture. While most transcriptomic studies have focused on host responses, the mechanisms by which generalist pathogens dynamically adapt their infection programs to diverse plant species remain poorly understood. Here, we present a comparative transcriptomic analysis of P. capsici during early-stage crown infection in four taxonomically and immunologically distinct hosts, Cucumis sativus, Cucumis melo, Capsicum annuum (CM334), and Solanum lycopersicum, via RNA-seq and multiphoton microscopy. Focusing on crown infections, the natural entry point for the pathogen, we reveal host-specific transcriptional programs that underpin differential infection strategies and outcomes. Our data show that P. capsici exhibits tightly regulated, host-dependent deployment of key virulence factors, including RxLR, NLP, and CRN, and elicitin effectors and reprograms its metabolism to exploit host-specific nutritional environments. In rapidly necrotizing hosts such as tomato, the pathogen induces glycolytic and fatty acid pathways while repressing immunogenic effectors. In contrast, cucurbits support prolonged biotrophic colonization, accompanied by the upregulation of carbohydrate metabolism and membrane transport genes. In the partially resistant chili pepper CM334, P. capsici shows signs of metabolic stress, cell wall remodeling, and effector repression, which is consistent with failed invasion. Functional validation via RNAi-mediated silencing of selected effectors revealed distinct roles in modulating virulence and host necrosis, confirming the functional relevance of the transcriptomic profiles. Co-expression network analysis uncovered discrete transcriptional modules associated with tissue-specific colonization, nutrient acquisition, and immune evasion. These results reveal how a generalist soil-borne pathogen finely tunes its gene expression in response to host-specific constraints, revealing conserved and host-specific transcriptional strategies that drive infection success or failure. This work provides mechanistic insight into adaptive virulence and expands our understanding of host-pathogen compatibility in eukaryotic microbes.

molecular biology↗