Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina
Xylella fastidiosa (Xf) is a Gram-negative bacterium that significantly threatens agricultural crops worldwide. In Argentina, severe symptoms resembling those of olive quick decline syndrome (OQDS) in Italy have been observed in Xf-infected olive orchards, primarily affecting the 'Arauco' variety in...
| Autores principales: | , , , , , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
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Springer
2025
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| Acceso en línea: | http://hdl.handle.net/20.500.12123/22690 https://link.springer.com/article/10.1007/s10658-024-02969-z https://doi.org/10.1007/s10658-024-02969-z |
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| author | Fernandez, Franco Daniel Arias-Giraldo, L.F. Tolocka, Patricia Guzman, Fabiana Olivares García, C. Roca, M.E. Otero, Maria Laura Conci, Luis Rogelio Landa, B.B. Haelterman, Raquel Mercedes |
| author_browse | Arias-Giraldo, L.F. Conci, Luis Rogelio Fernandez, Franco Daniel Guzman, Fabiana Haelterman, Raquel Mercedes Landa, B.B. Olivares García, C. Otero, Maria Laura Roca, M.E. Tolocka, Patricia |
| author_facet | Fernandez, Franco Daniel Arias-Giraldo, L.F. Tolocka, Patricia Guzman, Fabiana Olivares García, C. Roca, M.E. Otero, Maria Laura Conci, Luis Rogelio Landa, B.B. Haelterman, Raquel Mercedes |
| author_sort | Fernandez, Franco Daniel |
| collection | INTA Digital |
| description | Xylella fastidiosa (Xf) is a Gram-negative bacterium that significantly threatens agricultural crops worldwide. In Argentina, severe symptoms resembling those of olive quick decline syndrome (OQDS) in Italy have been observed in Xf-infected olive orchards, primarily affecting the 'Arauco' variety in La Rioja province. All Xf strains identified in Argentina, up to now, belong to the subspecies pauca (Xfp), with two sequence types (ST69 and ST78) identified so far. In this study, the complete circularized genomes of three Xf strains, isolated from olive (OLI17A, AM2-Angelina; from ST 69) and almond (ALM4; from ST78) infected trees in different regions in Argentina, were obtained using a hybrid assembly approach combining Oxford Nanopore Technologies and Illumina sequencing. Comparative genome analysis revealed collinearity between two strains (AM2-Angelina and OLI17A), while the ALM4 strain exhibited a large chromosome inversion in comparison to the AM2-Angelina and OLI17A genomes. The three genomes encoded numerous virulence genes involved in twitching motility and adhesion; although strain ALM4 lacked some anti-virulence factors such as prtA gene. Plasmids similar to those found in Xf strains isolated from citrus in South America and from olive trees in Europe were also identified. Comparative genomic analysis and phylogenetic reconstruction showed that the Xf Argentinean strains were genetically differentiated from those found in other countries although they formed a monophyletic group within the Xfp strains sequenced so far. Indeed, they were closely related to strains from citrus previously reported in Argentina and Brazil. The availability of these genomes will provide valuable insights for future studies on comparative genomics, virulence mechanisms, and epidemiology of Xf outbreaks in Argentina and elsewhere. |
| format | Artículo |
| id | INTA22690 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | INTA226902025-06-13T16:41:10Z Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina Fernandez, Franco Daniel Arias-Giraldo, L.F. Tolocka, Patricia Guzman, Fabiana Olivares García, C. Roca, M.E. Otero, Maria Laura Conci, Luis Rogelio Landa, B.B. Haelterman, Raquel Mercedes Xylella fastidiosa Aceituna Almendra Filogenia Genómica Comparativa Argentina Plasmidio Olives Almonds Phylogeny Comparative Genomics Plasmids Subspecies pauca Bacterial Plant Diseases Whole Genome Sequencing Pathogen Virulence Factors Xylella fastidiosa (Xf) is a Gram-negative bacterium that significantly threatens agricultural crops worldwide. In Argentina, severe symptoms resembling those of olive quick decline syndrome (OQDS) in Italy have been observed in Xf-infected olive orchards, primarily affecting the 'Arauco' variety in La Rioja province. All Xf strains identified in Argentina, up to now, belong to the subspecies pauca (Xfp), with two sequence types (ST69 and ST78) identified so far. In this study, the complete circularized genomes of three Xf strains, isolated from olive (OLI17A, AM2-Angelina; from ST 69) and almond (ALM4; from ST78) infected trees in different regions in Argentina, were obtained using a hybrid assembly approach combining Oxford Nanopore Technologies and Illumina sequencing. Comparative genome analysis revealed collinearity between two strains (AM2-Angelina and OLI17A), while the ALM4 strain exhibited a large chromosome inversion in comparison to the AM2-Angelina and OLI17A genomes. The three genomes encoded numerous virulence genes involved in twitching motility and adhesion; although strain ALM4 lacked some anti-virulence factors such as prtA gene. Plasmids similar to those found in Xf strains isolated from citrus in South America and from olive trees in Europe were also identified. Comparative genomic analysis and phylogenetic reconstruction showed that the Xf Argentinean strains were genetically differentiated from those found in other countries although they formed a monophyletic group within the Xfp strains sequenced so far. Indeed, they were closely related to strains from citrus previously reported in Argentina and Brazil. The availability of these genomes will provide valuable insights for future studies on comparative genomics, virulence mechanisms, and epidemiology of Xf outbreaks in Argentina and elsewhere. Instituto de Patología Vegetal Fil: Fernandez, Franco Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Fernandez, Franco Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Arias-Giraldo, L. F. Consejo Superior Investigaciones Científicas (CSIC). Instituto de Agricultura Sostenible (IAS); España Fil: Tolocka, Patricia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Tolocka, Patricia. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Guzman, Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi. Agencia de Extensión Rural Villa Dolores; Argentina Fil: Olivares, C. Consejo Superior Investigaciones Científicas (CSIC). Instituto de Agricultura Sostenible (IAS); España Fil: Roca, M.E. Servicio Nacional de Sanidad y Calidad Agroalimentaria (SENASA); Argentina Fil: Otero, Maria Laura. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Otero, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Conci, Luis Rogelio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Conci, Luis Rogelio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Landa, B.B. Consejo Superior Investigaciones Científicas (CSIC). Instituto de Agricultura Sostenible (IAS); España Fil: Haelterman, Raquel Mercedes. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Haelterman, Raquel Mercedes.Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina 2025-06-13T16:26:09Z 2025-06-13T16:26:09Z 2025-04 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/22690 https://link.springer.com/article/10.1007/s10658-024-02969-z 0929-1873 1573-8469 (online) https://doi.org/10.1007/s10658-024-02969-z eng info:eu-repograntAgreement/INTA/2019-PD-E4-I090-001, Análisis de patosistemas en cultivos agrícolas y especies forestales. Caracterización de sus componentes info:eu-repo/semantics/restrictedAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf Springer European Journal of Plant Pathology 171: 593–602 (2025) |
| spellingShingle | Xylella fastidiosa Aceituna Almendra Filogenia Genómica Comparativa Argentina Plasmidio Olives Almonds Phylogeny Comparative Genomics Plasmids Subspecies pauca Bacterial Plant Diseases Whole Genome Sequencing Pathogen Virulence Factors Fernandez, Franco Daniel Arias-Giraldo, L.F. Tolocka, Patricia Guzman, Fabiana Olivares García, C. Roca, M.E. Otero, Maria Laura Conci, Luis Rogelio Landa, B.B. Haelterman, Raquel Mercedes Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina |
| title | Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina |
| title_full | Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina |
| title_fullStr | Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina |
| title_full_unstemmed | Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina |
| title_short | Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina |
| title_sort | phylogenomic analysis of xylella fastidiosa subsp pauca strains from olive and almond trees in argentina |
| topic | Xylella fastidiosa Aceituna Almendra Filogenia Genómica Comparativa Argentina Plasmidio Olives Almonds Phylogeny Comparative Genomics Plasmids Subspecies pauca Bacterial Plant Diseases Whole Genome Sequencing Pathogen Virulence Factors |
| url | http://hdl.handle.net/20.500.12123/22690 https://link.springer.com/article/10.1007/s10658-024-02969-z https://doi.org/10.1007/s10658-024-02969-z |
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