Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids
Xylella fastidiosa (Xf) is a vascular plant pathogenic bacterium native to the Americas that is causing significant epidemics and economic losses in olive and almonds in Europe, where it is a quarantine pathogen. Since its first detection in 2013 in Italy, mandatory surveys across Europe revealed th...
| Autores principales: | , , , , , , , |
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| Formato: | article |
| Lenguaje: | Inglés |
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American Phytopathological Society (APS)
2023
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| Acceso en línea: | https://hdl.handle.net/20.500.11939/8665 https://apsjournals.apsnet.org/doi/10.1094/PHYTO-10-22-0396-A |
| _version_ | 1855032827637137408 |
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| author | Velasco-Amo, María P. Arias-Giraldo, Luis F. Román-Écija, Miguel de-la-Fuente, Leonardo Marco-Noales, Ester Moralejo, Eduardo Navas-Cortés, Juan A. Landa, Blanca B. |
| author_browse | Arias-Giraldo, Luis F. Landa, Blanca B. Marco-Noales, Ester Moralejo, Eduardo Navas-Cortés, Juan A. Román-Écija, Miguel Velasco-Amo, María P. de-la-Fuente, Leonardo |
| author_facet | Velasco-Amo, María P. Arias-Giraldo, Luis F. Román-Écija, Miguel de-la-Fuente, Leonardo Marco-Noales, Ester Moralejo, Eduardo Navas-Cortés, Juan A. Landa, Blanca B. |
| author_sort | Velasco-Amo, María P. |
| collection | ReDivia |
| description | Xylella fastidiosa (Xf) is a vascular plant pathogenic bacterium native to the Americas that is causing significant epidemics and economic losses in olive and almonds in Europe, where it is a quarantine pathogen. Since its first detection in 2013 in Italy, mandatory surveys across Europe revealed the presence of the bacterium also in France, Spain, and Portugal. Combining ONT and Illumina sequencing data, we assembled high-quality complete genomes of seven Xf subsp. fastidiosa strains isolated from different plants in Spain, the USA, and Mexico. Comparative genomic analyses discovered differences in plasmid content among strains, including plasmids that had been overlooked previously when using Illumina sequencing platform alone. Interestingly, in strain CFBP8073, intercepted in France from plants imported from Mexico, three plasmids were identified, including two (plasmid pXF-P1.CFBP8073 and pXF-P2.CFBP8073) not previously described in X. fastidiosa, and one (pXF5823.CFBP8073) almost identical to a plasmid described in a Xf strain from citrus. Plasmids found in the Spanish strains here were similar to those described previously in other strains from the same subspecies and ST1 isolated in the Balearic Islands and the USA. The genome resources from this work will assist in further studies on the role of plasmids in the epidemiology, ecology, and evolution of this plant pathogen. |
| format | article |
| id | ReDivia8665 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | American Phytopathological Society (APS) |
| publisherStr | American Phytopathological Society (APS) |
| record_format | dspace |
| spelling | ReDivia86652025-04-25T14:49:15Z Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids Velasco-Amo, María P. Arias-Giraldo, Luis F. Román-Écija, Miguel de-la-Fuente, Leonardo Marco-Noales, Ester Moralejo, Eduardo Navas-Cortés, Juan A. Landa, Blanca B. Bacterial pathogens Microbe-genome Sequencing Bioinformatics Ecology Xylella fastidiosa Plasmids Plant pathology Xylella fastidiosa (Xf) is a vascular plant pathogenic bacterium native to the Americas that is causing significant epidemics and economic losses in olive and almonds in Europe, where it is a quarantine pathogen. Since its first detection in 2013 in Italy, mandatory surveys across Europe revealed the presence of the bacterium also in France, Spain, and Portugal. Combining ONT and Illumina sequencing data, we assembled high-quality complete genomes of seven Xf subsp. fastidiosa strains isolated from different plants in Spain, the USA, and Mexico. Comparative genomic analyses discovered differences in plasmid content among strains, including plasmids that had been overlooked previously when using Illumina sequencing platform alone. Interestingly, in strain CFBP8073, intercepted in France from plants imported from Mexico, three plasmids were identified, including two (plasmid pXF-P1.CFBP8073 and pXF-P2.CFBP8073) not previously described in X. fastidiosa, and one (pXF5823.CFBP8073) almost identical to a plasmid described in a Xf strain from citrus. Plasmids found in the Spanish strains here were similar to those described previously in other strains from the same subspecies and ST1 isolated in the Balearic Islands and the USA. The genome resources from this work will assist in further studies on the role of plasmids in the epidemiology, ecology, and evolution of this plant pathogen. 2023-06-23T12:07:07Z 2023-06-23T12:07:07Z 2023 article publishedVersion Velasco-Amo, M. P., Arias-Giraldo, L. F., Román-Écija, M., Fuente, L. D. L., Marco-Noales, E., Moralejo, E., ... & Landa, B. B. (2023). Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids. Phytopathology®, 113(6), 1128-1132. 0031-949X 1943-7684 (e-ISSN) https://hdl.handle.net/20.500.11939/8665 10.1094/phyto-10-22-0396-a https://apsjournals.apsnet.org/doi/10.1094/PHYTO-10-22-0396-A en Support was provided by the HORIZON-CL6-2021-FARM2FORK-01 project BeXyl (Beyond Xylella, Integrated Management Strategies for Mitigating Xylella fastidiosa Impact in Europe; grant 101060593); the project ERTA2017-00004-C06-02 (Desarrollo de estrategias de erradicación, contención y control de X. fastidiosa en España) from the ‘Programa Estatal de I+D+I Orientada a los Retos de la Sociedad’ of the Spanish Government (AEI-INIA Spain); the Spanish Olive Oil Interprofessional; and the Thematic Interdisciplinary Platform on X. fastidiosa, PTI Sol-Xyl, from Consejo Superior de Investigaciones Científicas. Financial support from the Spanish Ministry of Agriculture and Fisheries to the Institute for Sustainable Agriculture is also acknowledged. L. De La Fuente was a recipient of a research fellowship awarded by the Organization for Economic Cooperation and Development, Cooperative Research Programme, during the writing of this manuscript. M. P. Velasco-Amo was a recipient of a contract financed by the Consejo Superior de Investigaciones Científicas Intramural Project 201840E111. Attribution-NonCommercial-NoDerivatives 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/ openAccess American Phytopathological Society (APS) electronico |
| spellingShingle | Bacterial pathogens Microbe-genome Sequencing Bioinformatics Ecology Xylella fastidiosa Plasmids Plant pathology Velasco-Amo, María P. Arias-Giraldo, Luis F. Román-Écija, Miguel de-la-Fuente, Leonardo Marco-Noales, Ester Moralejo, Eduardo Navas-Cortés, Juan A. Landa, Blanca B. Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids |
| title | Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids |
| title_full | Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids |
| title_fullStr | Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids |
| title_full_unstemmed | Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids |
| title_short | Complete circularized genome resources of seven strains of Xylella fastidiosa subsp. fastidiosa using hybrid assembly reveals unknown plasmids |
| title_sort | complete circularized genome resources of seven strains of xylella fastidiosa subsp fastidiosa using hybrid assembly reveals unknown plasmids |
| topic | Bacterial pathogens Microbe-genome Sequencing Bioinformatics Ecology Xylella fastidiosa Plasmids Plant pathology |
| url | https://hdl.handle.net/20.500.11939/8665 https://apsjournals.apsnet.org/doi/10.1094/PHYTO-10-22-0396-A |
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