Dual Transcriptomic Analysis of Isolates of <i>Phytophthora sansomeana</i> with Varying Levels of Aggressiveness Compared to <i>P. sojae</i> During a Time Course Infection Assay of Soybean

Phytophthora sansomeana was detected in several soybean root rot surveys in the United States alongside another well studied oomycete, P. sojae. We compared the transcriptomic response among three P. sansomeana isolates that differed in aggressiveness and P. sojae isolate OH25 to to the most aggressive P. sansomeana isolate in a moderately susceptible soybean using dual host-pathogen RNA-Seq. At each time point, relative pathogen read abundance was higher following inoculation with P. sojae than P. sansomeana. Differentially expressed genes (DEGs) relative to mycelial samples was more pronounced for P. sojae than P. sansomeana. More than a hundred genes were significantly upregulated across all three P. sansomeana isolates for all 3 time points. These included genes associated with cell wall degradation, jacalin-like lectin, NmrA-like family, one RxLR, and amino acid auxin permease family. For P. sansomeana, more genes annotated as CRN were downregulated and fewer Necrosis inducing peptides (NPL) were upregulated compared to P. sojae, which could explain in part the difference in necrosis symptom development between the two species. Additionally, P. sojae had more DEGs associated with pathogenicity than the most aggressive P. sansomeana isolate. Several key defense pathways were upregulated earlier in response to the three P. sansomeana isolates than to P. sojae, including glucosinolate and glutathione biosynthesis, sulfur and tropane, piperidine and pyridine alkaloid metabolism, which may also explain the reduced lesion sizes. These results provide a framework for using effector screening to select for effective host resistance against populations of both P. sansomeana and P. sojae.