Shotgun poplar disease diagnostic using next gen sequencing
B. DHILLON (1), N. Feau (1), R. C. Hamelin (1). (1) University of British Columbia, Vancouver, BC, Canada
Current advances in Next Generation Sequencing (NGS) technologies - higher sequence output coupled with lower costs - has resulted in a large number of genomes being sequenced. A wide variety of eukaryotic genomes from equally diverse environments can be rapidly sequenced and assembled. Our interest lies in dissecting this vast amount of NGS data from environmental samples for disease diagnostics, with the in the context of <i>Populus</i>-Dothideomycete and <i>Populus</i>-Urediniale interactions used as showcase. Once established, this data analysis pipeline could be virtually used for any host-pathogen system diagnosis. In addition to utilizing the existing genomic resources, we have sequenced the genomes of 12 poplar pathogens under the purview of Genome Canada funded TAIGA project. In a preliminary study, we have sequenced diseased hybrid poplar leaves harvested at the end of the growing season using Ion Torrent technology and analyzed the resulting dataset from two different field samples. By using genome-mapping approaches, we were able to assign reads to pathogen genomes that corresponded to visible disease symptoms on the poplar leaves. Most of the reads mapped to two of the most important poplar pathogens, <i>Mycosphaerella populorum</i> and <i>Melampsora occidentalis</i>. However, a large number of reads did not mapped onto these known sequenced genomes, an indication that more genomes will be required to provide a proper reference database and to identify potential new pathogens.
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