Putative pathogenicity genes of Phytophthora cinnamomi identified via RNA-Seq analysis of pre-infection structures

Phytophthora cinnamomi is an economically important oomycete that infects more than 3,000 plant species. We aimed to identify the repertoire of genes expressed during pre-infection stages by analysing an RNA-Seq library of cysts and germinating cysts of a P. cinnamomi isolate, originating from Persea americana. Over 70,000 transcripts were identified from 225,049 contigs, assembled from 13 million Illumina paired-end reads. Contaminant sequences were eliminated, resulting in 37,534 transcripts used in further analysis. A total of 1394 transcripts had a putative role in pathogenesis. Genes aiding in detoxification and metabolite transport (cytochrome P450 and ABC transporters) and protection against oxidative stress were most abundant, followed by the genes coding cell wall degrading enzymes. The transcript set included 44 putative RXLR effector genes and genes encoding elicitin and necrosis-inducing proteins. Expression patterns of seven putative pathogenicity genes (encoding RXLR-, necrosis-inducing Phytophthora protein 1 (NPP1), elicitin, polygalacturonase, cellulose binding and elicitor lectin (CBEL), mucin, and adhesion proteins) were assessed across four in vitro developmental stages of P. cinnamomi. High expression of these genes in zoospores suggests their functional importance in the subsequent developmental stage, germination of cysts, implying a role in pre-infection. This work is the first step towards understanding the molecular basis of infection strategies employed by P. cinnamomi.