Expression of GAF sensor, CAZymes, elicitins, and RXLRs differs markedly between two Phytophthora cactorum isolates.

The phytopathogen Phytophthora cactorum infects economically important herbaceous and woody plant species. The P. cactorum isolates differ in host-specificity; for example, strawberry crown rot is often caused by a specialized pathotype. Here we compared the transcriptomes of two P. cactorum isolates that differ in their virulence to garden strawberry (Pc407: high virulence; Pc440: low virulence). De novo transcriptome assembly and clustering of contigs resulted in 19 372 gene clusters. Two days after inoculation of Fragaria vesca roots, 3 995 genes were differently expressed between the P. cactorum isolates. One of the genes that were highly expressed only in Pc407 encodes a GAF sensor protein potentially involved in the membrane trafficking processes. Two days after inoculation, elicitins were highly expressed in Pc407 and lipid catabolism appeared to be more active than in Pc440. Of the carbohydrate-active enzymes, those that degrade pectin were often more highly expressed in Pc440, whereas members of glycosyl hydrolase family 1, potentially involved in the metabolism of glycosylated secondary metabolites, were more highly expressed in Pc407 at the time point studied. Differences were also observed among the RXLR effectors: Pc407 appears to rely on a smaller set of key RXLR effectors, whereas Pc440 expresses more numerous RXLRs. This study is the first step towards the understanding of the molecular basis of differences in the virulence of P. cactorum isolates. Identification of the key effectors is important as it enables effector-assisted breeding strategies towards crown rot resistant strawberry cultivars.