Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina

Autores
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
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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
Fuente
European Journal of Plant Pathology 171: 593–602 (2025)
Materia
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
Nivel de accesibilidad
acceso restringido
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/22690
Acceder
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oai_identifier_str oai:localhost:20.500.12123/22690
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network_name_str INTA Digital (INTA)
spelling Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in ArgentinaFernandez, Franco DanielArias-Giraldo, L.F.Tolocka, PatriciaGuzman, FabianaOlivares García, C.Roca, M.E.Otero, Maria LauraConci, Luis RogelioLanda, B.B.Haelterman, Raquel MercedesXylella fastidiosaAceitunaAlmendraFilogeniaGenómica ComparativaArgentinaPlasmidioOlivesAlmondsPhylogenyComparative GenomicsPlasmidsSubspecies paucaBacterial Plant DiseasesWhole Genome SequencingPathogen Virulence FactorsXylella 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 VegetalFil: Fernandez, Franco Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Fernandez, Franco Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Arias-Giraldo, L. F. Consejo Superior Investigaciones Científicas (CSIC). Instituto de Agricultura Sostenible (IAS); EspañaFil: Tolocka, Patricia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Tolocka, Patricia. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Guzman, Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi. Agencia de Extensión Rural Villa Dolores; ArgentinaFil: Olivares, C. Consejo Superior Investigaciones Científicas (CSIC). Instituto de Agricultura Sostenible (IAS); EspañaFil: Roca, M.E. Servicio Nacional de Sanidad y Calidad Agroalimentaria (SENASA); ArgentinaFil: Otero, Maria Laura. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Otero, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Conci, Luis Rogelio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Conci, Luis Rogelio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Landa, B.B. Consejo Superior Investigaciones Científicas (CSIC). Instituto de Agricultura Sostenible (IAS); EspañaFil: Haelterman, Raquel Mercedes. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Haelterman, Raquel Mercedes.Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaSpringer2025-06-13T16:26:09Z2025-06-13T16:26:09Z2025-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/22690https://link.springer.com/article/10.1007/s10658-024-02969-z0929-18731573-8469 (online)https://doi.org/10.1007/s10658-024-02969-zEuropean Journal of Plant Pathology 171: 593–602 (2025)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/2019-PD-E4-I090-001, Análisis de patosistemas en cultivos agrícolas y especies forestales. Caracterización de sus componentesinfo:eu-repo/semantics/restrictedAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-11-13T08:48:34Zoai:localhost:20.500.12123/22690instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-11-13 08:48:35.2INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv 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
spellingShingle Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina
Fernandez, Franco Daniel
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
title_short 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_sort Phylogenomic analysis of Xylella fastidiosa subsp. pauca strains from olive and almond trees in Argentina
dc.creator.none.fl_str_mv 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 Fernandez, Franco Daniel
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_role author
author2 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
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv 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
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
dc.description.none.fl_txt_mv 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
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.
publishDate 2025
dc.date.none.fl_str_mv 2025-06-13T16:26:09Z
2025-06-13T16:26:09Z
2025-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
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info:ar-repo/semantics/articulo
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status_str publishedVersion
dc.identifier.none.fl_str_mv 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
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
identifier_str_mv 0929-1873
1573-8469 (online)
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/2019-PD-E4-I090-001, Análisis de patosistemas en cultivos agrícolas y especies forestales. Caracterización de sus componentes
dc.rights.none.fl_str_mv 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)
eu_rights_str_mv restrictedAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv European Journal of Plant Pathology 171: 593–602 (2025)
reponame:INTA Digital (INTA)
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instname_str Instituto Nacional de Tecnología Agropecuaria
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repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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