Advancing detection, genomics, and secretome analysis of oomycete pathogens Phytophthora capsici and Phytopythium vexans to explore mechanisms of pathogenesis and biocontrol solutions

Soilborne oomycete pathogens pose persistent challenges to vegetable production systems, particularly in Ontario, Canada, where Phytophthora capsici and the recently reported Phytopythium vexans have emerged as significant threats. Understanding the molecular mechanisms underlying their pathogenicity is critical for developing informed, site-specific disease management strategies. This thesis integrates comparative genomics, effector biology, and molecular diagnostics to enhance our understanding of their pathogenicity and support effective disease management. The first component of this work focuses on P. capsici, where whole-genome sequencing of two Canadian isolates (55330 and 55898) revealed compact genomes yet retained a broad array of RxLR and CRN effectors. Comparative analyses with reference strains LT263 and LT1534 v11.0 uncovered both conserved and unique effectors, suggesting that local adaptation may be shaping pathogenic potential in response to regional crop pressures. Building on this, the second component shifts to P. vexans, a novel strain recently reported in Ontario from apple tree soil. The SS21 P. vexans strain genome was sequenced and compared with the only two openly available strains HF1(China), and (CBS 119.80) (Iran). The genomic analysis reveals similar genome between the Canadian strain SS21 and the reference genomes, additionally SS21 displayed a reduce CAZymes, RxLR and CRN effectors, suggesting a niche adaptation to a specific Canadian agro-ecosystem. The final component of this thesis focuses on the development of an amplitude-based multiplex droplet digital PCR (ddPCR) assay. Designed for simultaneous quantification of P. capsici, Trichoderma asperellum, and Trichoderma gamsii in soil, this assay was validated in field trials and offers high sensitivity and specificity. The assay displayed a high sensitivity with a limit of detection of 1 pg/µL DNA. The use of multiplex ddPCR offers practical solution for monitoring pathogen and biocontrol populations in complex soil environments.

Name thesis:degree_name

Ph.D. Biological Sciences

Level thesis:degree_level

Doctoral

Discipline thesis:degree_discipline

Faculty of Mathematics and Science

Department dc:contributor.department

Department of Biological Sciences

Grantor dc:publisher

Brock University

Year dc:date.issued

2025

Author dc:creator

• Villanueva Oscar

Advisors dc:contributor.advisor

• Castle Alan
• Ellouz Oualid

• NATURAL SCIENCES::Chemistry::Biochemistry::Molecular biology

Language dc:language.iso

eng

Handle dc:identifier.uri

https://hdl.handle.net/10464/19386

OAI identifier oai:identifier

oai:brocku.scholaris.ca:10464/19386