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Taiga Forest Health

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Genome Sequencing

Our objective is to sequence the genomes of forest pathogens and to use available and newly generated genomics resources to compare genomes within and between taxonomic groups, generating core gene sets unique to each group. Validated gene sets will then be used to develop detection and monitoring assays.

 

 

Targeted groups and species

Our research will focus on genome sequencing of forest pathogens in three targeted groups within the strategically important orders of tree rusts (Pucciniales), tree blights and cankers (Dothideomycetes), and the sudden oak death and related pathogens (Oomycetes).

 

The list of species to be sequenced was prioritized using the following criteria*:

1) Type of damage caused;

2) Economic importance to Canada (or elsewhere);

3) Presence on list of unwanted invasive pathogens;

4) Phylogenetic diversity within each group

*As utilized by the regulatory agencies European and Mediterranean Plant Protection Organization (EPPO), North American Plant Protection Organization (NAPO) and Canadian Food Inspection Agency (CFIA).

Sequencing platform and Genome Assembly

Using the Illumina sequencing platform at Canada’s Michael Smith Genome Sciences Centre (GSC), these genomes will be sequenced to a minimum depth of 40-200X, depending on the actual estimated genome size(ranging from 30Mb to 100 Mb, for Dothideomycetes and Pucciniales respectively). In parallel, for each genome sequenced we will sequence several populations of mRNA, to help improve automated protein model predictions. De-novo assemblies and gene calling-protein model predictions will be carried out at GSC with pipelines already improved on fungal genomes.

Comparative pipeline

We will use available and newly generated genomics resources to compare genomes within and between groups, generating core gene sets unique to each group. We will also develop and use bioinformatics pipelines to screen genomes for gene families with important functions in plant pathogenicity and host adaptation as small secreted proteins and effectors (see below), mycotoxin production, plant cell-wall degradation, plant-metabolites uptake.

Latest genome sequences released