Picture by Braham Dhillon
Mycosphaerella populorum (canker disease of poplar) - Native to northeastern North America
Picture by Guillaume Bilodeau
Phytophthora ramorum (Sudden oak death) - Repeatedly introduced and eradicated in British Columbia
Robert L. Anderson, USDA Forest Service, Bugwood.org;
Cronartium ribicola (White Pine Blister Rust) - The most important disease of white pines, one of the most valuable North American softwoods.
Using the Illumina sequencing platform at Canada’s Michael Smith Genome Sciences Centre (GSC), low coverage whole-genome re-sequencing of individuals from different populations will be sequenced, with a minimum average depth of 3-19X, depending on the actual estimated genome size: M. populorum (~30 Mb), P. ramorum (~65Mb) and, C. ribicola (~100 Mb).
We will use available and newly generated genomics resources to perform strain-specific genome-wide SNP profiling in order to determine origin of introduction and routes of spread. Actually, from assembled contigs, we will use the MAQ software to: (1) determine minimum and maximum read depth, minimum consensus quality, proximity to an indel; (2) perform SNP calling.
These analyses will be used to generate genomics-based migration maps for the targeted groups of pathogens. Such maps can be used in conjunction with the diagnostic arrays for improved pest risk assessment, to help determine appropriate phytosanitary measures and inform regulatory processes.
Our objective is to re-sequence the genomes of multiple isolates for three forest pathogens to determine origin of introduction and routes of spread, and to prevent further introductions. Multiple assembled genomes will be used to generate strain-specific genome-wide SNP profiles in order to determine origin of introduction and routes of spread. The generated data will also serve as a reference for later comparison of epidemiological strains and for development of SNP genotyping assays.
Our research will focus on two recently introduced invasive pathogens (Mycosphaerella populorum and Phytophthora ramorum), and one pathogen introduced over a century ago that is still expanding to new hosts and geographic range (Cronartium ribicola).