Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles

[EN] Phytophthora cinnamomi is a hemibiotrophic oomycete causing Phytophthora root rot in over 5,000 plant species, threatening natural ecosystems, forestry, and agriculture. Genomic studies of P. cinnamomi are limited compared to other Phytophthora spp. despite the importance of this destructive an...

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Autores: Shands, Aidan C., Xu, Guangyuan, Belisle, Rodger J., Seifbarghi, Shirin, Jackson, Natasha, Cano, Liliana M., Manosalva, Patricia M., Bombarely A
Tipo de recurso: artículo
Fecha de publicación:2024
País:España
Institución:Universitat Politècnica de València (UPV)
Repositorio:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
Idioma:inglés
OAI Identifier:oai:riunet.upv.es:10251/208042
Acceso en línea:https://riunet.upv.es/handle/10251/208042
Access Level:acceso abierto
Palabra clave:Phytophthora
Oomycete
Phytophthora root rot
Two-speed genome
Effectors
Cell wall-degrading enzymes
RXLRs
Transcriptome analyses
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spelling Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profilesShands, Aidan C.Xu, GuangyuanBelisle, Rodger J.Seifbarghi, ShirinJackson, NatashaCano, Liliana M.Manosalva, Patricia M.Bombarely APhytophthoraOomycetePhytophthora root rotTwo-speed genomeEffectorsCell wall-degrading enzymesRXLRsTranscriptome analyses[EN] Phytophthora cinnamomi is a hemibiotrophic oomycete causing Phytophthora root rot in over 5,000 plant species, threatening natural ecosystems, forestry, and agriculture. Genomic studies of P. cinnamomi are limited compared to other Phytophthora spp. despite the importance of this destructive and highly invasive pathogen. The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing. Genome sizes were estimated by flow cytometry and assembled de novo to 140-141 Mb genomes with 21,111-21,402 gene models. Genome analyses revealed that both isolates exhibited complex heterozygous genomes fitting the two-speed genome model. The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate. Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana, and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors. Overall, our results suggested that clonal P. cinnamomi isolates employ similar strategies as other Phytophthora spp. to increase phenotypic diversity (e.g., polyploidization, gene duplications, and a bipartite genome architecture) to cope with environmental changes. Our study also provides insights into common and host-specific P. cinnamomi infection strategies and may serve as a method for narrowing and selecting key candidate effectors for functional studies to determine their contributions to plant resistance or susceptibility.The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was funded by the UC MEXUS-CONACYT Collaborative Grants (grant number CN-19-112), the USDA/NIFA-AFRI, Pests and Beneficial Species in Agricultural Production Systems (grant number 2020-67014-31859), the USDA-NIFA, Specialty Crop Research Initiative (grant number 2020-51181-32198), and the California Avocado Commission (grant number 65211).Frontiers Media SACalifornia Avocado CommissionU.S. Department of AgricultureConsejo Nacional de Humanidades, Ciencias y Tecnologías, MéxicoRepositorio Institucional de la Universitat Politècnica de València Riunet20242024-08-15journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://riunet.upv.es/handle/10251/208042reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valénciainstname:Universitat Politècnica de València (UPV)InglésengU.S. Department of Agriculture https://doi.org/10.13039/100000199 2020-67014-31859CONAHCYT CONAHCYT CONACYTCalifornia Avocado Commission California Avocado Commission 65211open accesshttp://purl.org/coar/access_right/c_abf2Reconocimiento (by)http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:riunet.upv.es:10251/2080422026-06-13T07:49:27Z
dc.title.none.fl_str_mv Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles
title Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles
spellingShingle Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles
Shands, Aidan C.
Phytophthora
Oomycete
Phytophthora root rot
Two-speed genome
Effectors
Cell wall-degrading enzymes
RXLRs
Transcriptome analyses
title_short Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles
title_full Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles
title_fullStr Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles
title_full_unstemmed Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles
title_sort Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles
dc.creator.none.fl_str_mv Shands, Aidan C.
Xu, Guangyuan
Belisle, Rodger J.
Seifbarghi, Shirin
Jackson, Natasha
Cano, Liliana M.
Manosalva, Patricia M.
Bombarely A
author Shands, Aidan C.
author_facet Shands, Aidan C.
Xu, Guangyuan
Belisle, Rodger J.
Seifbarghi, Shirin
Jackson, Natasha
Cano, Liliana M.
Manosalva, Patricia M.
Bombarely A
author_role author
author2 Xu, Guangyuan
Belisle, Rodger J.
Seifbarghi, Shirin
Jackson, Natasha
Cano, Liliana M.
Manosalva, Patricia M.
Bombarely A
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv California Avocado Commission
U.S. Department of Agriculture
Consejo Nacional de Humanidades, Ciencias y Tecnologías, México
Repositorio Institucional de la Universitat Politècnica de València Riunet
dc.subject.none.fl_str_mv Phytophthora
Oomycete
Phytophthora root rot
Two-speed genome
Effectors
Cell wall-degrading enzymes
RXLRs
Transcriptome analyses
topic Phytophthora
Oomycete
Phytophthora root rot
Two-speed genome
Effectors
Cell wall-degrading enzymes
RXLRs
Transcriptome analyses
description [EN] Phytophthora cinnamomi is a hemibiotrophic oomycete causing Phytophthora root rot in over 5,000 plant species, threatening natural ecosystems, forestry, and agriculture. Genomic studies of P. cinnamomi are limited compared to other Phytophthora spp. despite the importance of this destructive and highly invasive pathogen. The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing. Genome sizes were estimated by flow cytometry and assembled de novo to 140-141 Mb genomes with 21,111-21,402 gene models. Genome analyses revealed that both isolates exhibited complex heterozygous genomes fitting the two-speed genome model. The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate. Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana, and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors. Overall, our results suggested that clonal P. cinnamomi isolates employ similar strategies as other Phytophthora spp. to increase phenotypic diversity (e.g., polyploidization, gene duplications, and a bipartite genome architecture) to cope with environmental changes. Our study also provides insights into common and host-specific P. cinnamomi infection strategies and may serve as a method for narrowing and selecting key candidate effectors for functional studies to determine their contributions to plant resistance or susceptibility.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024-08-15
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://riunet.upv.es/handle/10251/208042
url https://riunet.upv.es/handle/10251/208042
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv U.S. Department of Agriculture https://doi.org/10.13039/100000199 2020-67014-31859
CONAHCYT CONAHCYT CONACYT
California Avocado Commission California Avocado Commission 65211
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reconocimiento (by)
http://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reconocimiento (by)
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Frontiers Media SA
publisher.none.fl_str_mv Frontiers Media SA
dc.source.none.fl_str_mv reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
instname:Universitat Politècnica de València (UPV)
instname_str Universitat Politècnica de València (UPV)
reponame_str RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
collection RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
repository.name.fl_str_mv
repository.mail.fl_str_mv
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