Characterization of Stripe Rust Isolates from Western Canada Using NGS

The stripe (yellow) rust pathogen Puccinia striiformis f. sp. tritici (Pst) is a world-wide prevailing disease of wheat that has an impact on food security. Pst is highly aggressive and quickly evolves to generate new races to overcome host resistance genes. The genome size of this pathogen is ≈117 Mb. Races that predominated during 1960-2000 were adapted to the cooler temperatures of the intermountain regions of western North America. Since 2000, races that are adapted to the warmer regions of the western Great Plains have become widespread. The goals of this project are to identify genetic elements in Pst that are related to race virulence or temperature adaptation. Genomic DNA from 14 strains of Pst sampled between 1984 and 2012 has been sequenced with deep coverage using the Illumina technology (HiSeq & MiSeq). Sequence reads were mapped to reference strains Pst78 and CY32. Sequence complements from pre-year 2000 and post-year 2000 (post2K) isolates of both mapped and unmapped reads were compared using both genomic and transcriptomic references. The annotated new and enriched GO terms identified in post2K isolates from the mapped and unmapped reads included different genes present in cell wall and plasma membrane  or that are involved in transport and signaling, response to exogenous molecules and RNA metabolism. Reorganization of retrotransposons and detection of new retrotransposons were observed. Non-annotated sequenced encoding small proteins putatively representing potential effectors were also identified in post2K isolates.