Infection by Phytophthora parasitica induces distinct classes of small RNA in Arabidopsis roots

Zhong CC1,2, Wang MB2 and Shan WX1

  1. Northwest Agricultural and Forestry University, Yangling, Shaanxi, China.
  2. CSIRO Agriculture and Food, Clunies Ross Street, Canberra, ACT 2601, Australia.

Oomycetes, including Phytophthora, are eukaryotic microorganisms that are evolutionarily similar to algae, and can cause damages to both agricultural production and natural ecosystems. Small RNAs (sRNAs) are important regulators in eukaryotes, and have been implicated in plant defence responses to pathogens. However, how sRNAs contribute to plant-Phytophthora interactions remains unclear. In this study we used Arabidopsis thaliana-Phytophthora parasitica as a pathosystem to investigate the role of sRNAs in plant response to Phytophthora. We analysed sRNA profiles in the roots of Arabidopsis plants infected with P. parasitica at successive stages of infection. sRNA deep sequencing resulted in approximately 10 million reads for each infection stage, of which around 70% matched perfectly to the Arabidopsis genome. Comparative analysis of sRNA population between infected and uninfected roots revealed a general induction of 21-nt and 24-nt canonical sRNAs at the cysts germination (3 hpi) and haustoria appearing (6 hpi) stages, and a strong induction of a novel class of 28-nt sRNAs at abundant haustoria (12 hpi) and hyphae colonization (24 hpi) stages. Of the canonical sRNAs, we identified several differentially expressed miRNAs that have target genes involved in plant immunity and differentially expressed in infected roots. In addition, we identified 24-nt small interfering RNAs (siRNAs) that target promoters or introns of Arabidopsis genes that showed differential expression upon Phytophthora infection, suggesting the involvement of siRNA-directed DNA methylation in Phytophthora response. The 28-nt size class are derived mainly from intergenic regions, and their biogenesis appears to be linked with the RNA-directed DNA methylation pathway. Details of the findings will be presented.