Identification And Analysis Of Small Rans In Phytopthora Sojae And Phytophthora Parasitica

Small non-coding RNAs are a group of important regulators involved in post transcription regulation in eukaryotes, including microRNA, siRNA that are widely exist in animal and plant, and piRNA identified from mammalian germ lines. Oomycete pathogens, which are morphologically similar with fungi but are distinct in evolution, cause severe damages to agricultural production and ecosystems. Because of their wide existence and important regulation function, small RNAs are well studied recently in animals and plants, however, little is known in oomycetes.Phytophthora sojae and Phytophthora parasitica were used in this study to understand small RNA biology in oomycete pathogens, by cloning and deep sequencing approaches. The results showed that P. sojae and P. parasitica encode a distinct class of small RNAs with a peak at 25nt, suggesting the presence of nucleases required for producing small RNAs. The genome mapping of small RNAs showed distinct hot and cold spots of transcription, suggesting additional evidence for the presence of small RNAs in Phytophthora and for bioinformatic prediction of small non-coding RNAs. By classification, Phytophthra genome were shown to encode a variety of small non-coding RNAs. By bioinformatic prediction and Northern blotting validation, several candidate small RNAs were identified, including that derived from transfer and ribosomal RNAs. Small RNA cloning also demonstrated the existence of tRNA and rRNA derived small RNAs. Analysis of the expression patterns of tRNA derived small RNAs Pso4367 and Ppa10815 in P. sojae and P. parasitica showed that their increased accumulation in mycelia, sporangia and oospores, down-regulation during plant infection, and less detectable in cysts and germinating cyst.In this study, small non-coding RNAs in P. sojae and P. parasitica were identified and preliminarily analyzed for their classes and characters. The identification of several candidate small RNAs faciliates further understanding of small RNAs in oomycete biology and in plant-oomycete interaction.