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...
| Authors: | ; ; ; ; ; ; ; |
|---|---|
| Format: | Article |
| Publication date: | 2024 |
| Country: | España |
| Institution: | Universitat Politècnica de València (UPV) |
| Repository: | RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia |
| Language: | English |
| OAI Identifier: | oai:riunet.upv.es:10251/208042 |
| Online Access: | https://riunet.upv.es/handle/10251/208042 |
| Access Level: | Open access |
| Keyword: | Phytophthora Oomycete Phytophthora root rot Two-speed genome Effectors Cell wall-degrading enzymes RXLRs Transcriptome analyses |
| _version_ | 1878739505710628864 |
|---|---|
| author | Shands, Aidan C. |
| 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 |
| author_browse | Belisle, Rodger J. Bombarely A Cano, Liliana M. Jackson, Natasha Manosalva, Patricia M. Seifbarghi, Shirin Shands, Aidan C. Xu, Guangyuan |
| 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 |
| collection | RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia |
| 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. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | ES_c2c28bb8ffdcdc27e48a33db819ee991 |
| institution | Universitat Politècnica de València (UPV) |
| instname_str | Universitat Politècnica de València (UPV) |
| language | eng |
| network_acronym_str | ES |
| network_name_str | España |
| oai_identifier_str | oai:riunet.upv.es:10251/208042 |
| publishDate | 2024 |
| publishDateSort | 2024 |
| publisher | Frontiers Media SA |
| publisherStr | Frontiers Media SA |
| reponame_str | RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia |
| spelling | Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles Shands, Aidan C. Xu, Guangyuan Belisle, Rodger J. Seifbarghi, Shirin Jackson, Natasha Cano, Liliana M. Manosalva, Patricia M. Bombarely A Phytophthora Oomycete Phytophthora root rot Two-speed genome Effectors Cell wall-degrading enzymes RXLRs Transcriptome 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 SA https://riunet.upv.es/handle/10251/208042 |
| 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 | 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_short | 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 |
| topic | Phytophthora Oomycete Phytophthora root rot Two-speed genome Effectors Cell wall-degrading enzymes RXLRs Transcriptome analyses |
| topic_facet | Phytophthora Oomycete Phytophthora root rot Two-speed genome Effectors Cell wall-degrading enzymes RXLRs Transcriptome analyses |
| url | https://riunet.upv.es/handle/10251/208042 |