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 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