RNA-seq for comparative transcript profiling of Phytophthora capsici during its interaction with Arabidopsis thaliana

Phytophthora capsici, a highly dynamic and destructive oomycete pathogen, causes devastating diseases on a wide range of plants worldwide. However, the detailed molecular mechanisms of pathogenicity is still largely unclear. In this study, three different mRNA pool libraries were constructed from its developmental stage, early or late infection stage of the model plant Arabidopsis thaliana, and then were investigated by the RNA-Seq approach. The results demonstrated that 1456 novel transcripts that had not linked to any annotated gene were identified, and 296 genes were found to undergo alternative splicing. Comparative analysis of three different libraries further showed that distinct transcriptional changes of pathogenicity genes were found. A large number of genes containing cell wall degrading enzymes, major facilitator superfamily genes and cytochrome P450 genes were highly induced during infection. In addition, several types of well-known effectors including RxLR, CRN, Elicitin and NLP proteins also showed high transcript abundances during infection. The transcriptional levels of six effector genes during the infection process were further validated by qRT-PCR. Collectively, this study provides a basic understanding of pathogenic mechanisms of P. capsici during the interaction with plants.