Page 194 - Plant Canada 2024 Proceeding

PLANT CANADA 2024

[O177] DE NOVO WHOLE-GENOME ASSEMBLIES AND A COMPARATIVE PANGENOME
ANALYSIS OF THE SOILBORNE PLANT PATHOGEN PLASMODIOPHORA BRASSICAE. Sandra M.
Velasco-Cuervo , Yoann Aigu , Leonardo Galindo-González , Sheau-Fang Hwang and Stephen E.
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Strelkov . Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB,
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Canada; and Ottawa Plant Laboratory (Fallowfield), Science Branch, Canadian Food Inspection Agency,
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Ottawa, ON, Canada
Correspondence to: sandrama@ualberta.ca

Plasmodiophora brassicae causes clubroot, a soilborne disease of canola (Brassica napus) and other
crucifers. Pathogen isolates are classified into pathotypes based on their virulence on the hosts of
the Canadian Clubroot Differential (CCD) set. Genomic resources for P. brassicae, especially for
Canadian pathotypes, are currently limited. The main objective of this project is to identify differences
between pathotypes of P. brassicae, facilitating molecular identification and enhancing understanding of
the diversity and relationships between them. High Fidelity (HiFi) sequencing was utilized to
generate long-reads and construct de novo whole-genome assemblies for single-spore isolates of P.
brassicae, representing seven important pathotypes. The assemblies currently have an average
completeness of 80.84% based on BUSCO analysis, and an average genome size of 24.55 Mb. The
first annotation round for each assembly resulted in an average of 30.05% of the genome annotated as
repetitive regions. A pangenome was constructed using the seven P. brassicae assemblies, revealing a
core genome that accounted for 66.7% of the total genome length and an accessory genome comprising
33.92%. Nine-hundred eighty-one structural variants (897 bi-allelic and 84 multi-allelic) were identified,
with an average of 60,000 SNPs observed between the assemblies. A comprehensive genome
annotation is underway. Selected SNPs and structural variants will be tested through Sanger sequencing
to validate the results from the bioinformatic analyses. This approach will enable the identification of
polymorphic regions and development of a metabarcoding assay for P. brassicae pathotype detection.
These findings can also be integrated into studies of the pathogen's evolution and genomic architecture.

[O178] GENOMIC INVESTIGATION OF WESTERN CANADIAN APHANOMYCES EUTEICHES
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ISOLATES FROM MULTIPLE HOST LEGUME CROPS. Zelalem Taye , Jamuna Paudel , Lou Kun ,
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Cormier Trista , Ethan Done , Jennifer Town , Syama Chatterton , Michelle Hubbard , Hossein Borhan
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and Nicholas Larkan . Saskatoon RDC, Agriculture & Agri-Food Canada, Saskatoon, Saskatchewan,
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Canada; Lethbridge RDC, Agriculture & Agri-Food Canada, Lethbridge, Alberta, Canada; and Swift
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Current RDC, Agriculture & Agri-Food Canada, Swift Current, Saskatchewan, Canada
Correspondence to: zelalem.taye@agr.gc.ca

Aphanomyces root rot (ARR) is a significant challenge to pea cultivation in Western Canada. Its impact is
also progressively extending to other crops like lentils and dry beans. Recent advances in pathology
testing involving Aphanomyces euteiches isolates from diverse host crops have revealed intriguing
nuances suggesting the existence of varying degrees of host specificity within distinct populations of A.
euteiches. In addition, metagenomic investigations have also unveiled a higher level of genetic diversity
within field populations than previously expected. These insights into the complex nature of ARR
underscore the need for comprehensive research to help inform management strategies in the region. In
the pursuit of identifying resistance possibilities and other management options in different host crops and
environments, and advancing molecular diagnostic techniques for pathogen monitoring, it is crucial to
gain insights into the population dynamics of A. euteiches and any potential host-specific relationships
linked to pathogen genotype. In this presentation, diversity of A. euteiches in the region, genomes of
isolates from pea and lentil, and lesson learned from pathology of the pathogen and future work aimed at
characterizing A. euteiches populations across Western Canada will be presented.

[O179] SINGLE-CELL DNA SEQUENCING OF PLASMODIOPHORA BRASSICAE REVEALS CLONAL
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CHARACTERISTICS. A. Sedaghatkish , B. D. Gossen , and M. R. McDonald . Department of Plant
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Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada; and Saskatoon Research and
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Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
Correspondence to: asedagha@uoguelph.ca

This study explored the genomic variation in Plasmodiophora brassicae Wor., an obligate Chromist
pathogen responsible for clubroot disease in canola (Brassica napus L.) and other brassica crops. The
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