{"id":{"repo_id":"brock","oai_identifier":"oai:brocku.scholaris.ca:10464/19386"},"canonical_url":"https://search.dev.ndltd.org/etd/brock/oai:brocku.scholaris.ca:10464/19386","repository":{"repo_id":"brock","name":"Brock University","base_url":"https://brocku.scholaris.ca/server/oai/request"},"display":{"title":"Advancing detection, genomics, and secretome analysis of oomycete pathogens Phytophthora capsici and Phytopythium vexans to explore mechanisms of pathogenesis and biocontrol solutions","abstract":"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.","abstract_html":"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.","abstract_has_math":false,"creators":["Villanueva Oscar"],"institution":"Brock University","degree_name":"Ph.D. Biological Sciences","degree_level":"Doctoral","degree_discipline":"Faculty of Mathematics and Science","degree_department":"Department of Biological Sciences","school":null,"contributors":[],"advisors":["Castle Alan","Ellouz Oualid"],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-05-23T19:39:52Z","date_published":"2025-05-23T19:39:52Z","updated_at":"2026-07-24T01:23:20Z","subjects":["NATURAL SCIENCES::Chemistry::Biochemistry::Molecular biology"],"languages":["eng"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/10464/19386","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Castle Alan","Ellouz Oualid"]},{"key":"dc:contributor.department","label":"Department","values":["Department of Biological Sciences"]},{"key":"dc:creator","label":"Author","values":["Villanueva Oscar"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2025-05-23T19:39:52Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2025-05-23T19:39:52Z"]},{"key":"dc:date.issued","label":"Date","values":["2025-05-23T19:39:52Z"]},{"key":"dc:publisher","label":"Institution","values":["Brock University"]},{"key":"dc:type","label":"Dc Type","values":["Electronic Thesis or Dissertation"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Faculty of Mathematics and Science"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Doctoral"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D. Biological Sciences"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["NATURAL SCIENCES::Chemistry::Biochemistry::Molecular biology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["eng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/10464/19386"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["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."]},{"key":"dc:title","label":"Title","values":["Advancing detection, genomics, and secretome analysis of oomycete pathogens Phytophthora capsici and Phytopythium vexans to explore mechanisms of pathogenesis and biocontrol solutions"]}]}],"canonical_facts":{"dc:contributor.advisor":["Castle Alan","Ellouz Oualid"],"dc:contributor.department":["Department of Biological Sciences"],"dc:creator":["Villanueva Oscar"],"dc:date.accessioned":["2025-05-23T19:39:52Z"],"dc:date.available":["2025-05-23T19:39:52Z"],"dc:date.issued":["2025-05-23T19:39:52Z"],"dc:description.abstract":["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."],"dc:identifier.uri":["https://hdl.handle.net/10464/19386"],"dc:language.iso":["eng"],"dc:publisher":["Brock University"],"dc:subject":["NATURAL SCIENCES::Chemistry::Biochemistry::Molecular biology"],"dc:title":["Advancing detection, genomics, and secretome analysis of oomycete pathogens Phytophthora capsici and Phytopythium vexans to explore mechanisms of pathogenesis and biocontrol solutions"],"dc:type":["Electronic Thesis or Dissertation"],"thesis:degree_discipline":["Faculty of Mathematics and Science"],"thesis:degree_level":["Doctoral"],"thesis:degree_name":["Ph.D. Biological Sciences"]},"updated_at":"2026-07-24T01:23:20Z"}