Transcriptome analysis, using RNA-seq, of Lomandra longifolia roots infected with Phytophthora cinnamomi reveals the complexity of the resistance response

The plant pathogen Phytophthora cinnamomi is the causal agent of disease in numerous species, is a major threat to natural vegetation and has economic impacts in agriculture. The pathogen principally invades the root system which, in susceptible species, is rapidly colonised and functionally destroyed. Few species are resistant, however, where resistance is expressed the pathogen is restricted to small, localised lesions. The molecular mechanisms that underpin this response in resistant species are not well understood. Lomandra longifolia, an Australian native species is highly resistant to P. cinnamomi. In an earlier study, we had shown induction of resistance-related components such as callose, lignin and hydrogen peroxide (H2 O2 ) in L. longifolia roots that had been inoculated with P. cinnamomi. Here, in order to further identify during the very early stages of infection the molecular components and regulatory networks that may trigger resistance, a comprehensive root transcriptome analysis was performed using next generation sequencing. Overall, eighteen cDNA libraries were produced generating 52.8 GB 126 base pair reads, which were de novo assembled into contigs. Differentially expressed genes (DGEs) were identified allowing the identification of infection-responsive candidate genes that were putatively related to resistance and from this set ten were selected for qRT-PCR to validate the RNA-seq expression value. Further analysis of individual candidates revealed that many were involved in PAMP-triggered immunity (PTI) (pattern recognition receptors, glutathione S-transferase, callose synthases, pathogenesis-related protein-1, and mitogen activated protein kinases) and effector-triggered immunity (ETI) (NBS-LRR, signalling genes, transcription factors and anti-pathogenic compound synthase genes). As these candidate genes or mediated components activate different defence signalling systems, they may have potential for investigation of novel approaches to disease control and in transgenic approaches for improvement, in susceptible species, of resistance to P. cinnamomi.