Plant & Animal Genomes XIX Conference

January 15-19, 2011
Town & Country Convention Center
San Diego, CA

Phytophthora Small RNA Biology

SR Bollmann¹ , N Fahlgren² , CM Sullivan² , CM Press¹ , JC Carrington² , Niklaus J Grunwald¹

¹  USDA ARS, 3420 NW Orchard Ave., Corvallis, OR 97330, USA

²  Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331

Gene regulation by small RNA pathways is highly conserved among eukaryotes, although little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora, a genus of fungal-like oomycetes, contains some of the most devastating plant pathogens, causing multibillion dollar damage to crops, ornamental plants, and natural environments. We used high-throughput pyrosequencing and sequencing-by-synthesis to profile small RNAs. Analysis of these data revealed several candidate MIRNA genes from one gene family that are conserved in Phytophthora. In addition, a large number of siRNA-generating loci were identified. Two Dicer homologs, DCL1 and DCL2, and one RDR homolog were cloned and annotated from P. sojae, and gene expression analysis revealed only minor changes in transcript levels among different lifestages and infection timepoints. Oomycete DCL1 homologs clustered with animal and plant Dicer homologs, whereas oomycete DCL2 homologs clustered basally to the tree along with Drosha homologs. Phylogenetic analysis of the RDR homologs confirmed a previous study which suggested the last common eukaryote ancestor possessed three RDR homologs which were selectively retained or lost in later lineages. We analyzed the altered domain structure of oomycete Dicer and RDR homologs, specifically focusing on the proposed domain swapping of the DEAD-box helicase domain from Dicer to RDR. Implications of the alternate gene structure are discussed, and possible roles of the two oomycete Dicer homologs are proposed.