Race-specific genotypes of Pseudomonas syringae pv. tomato are defined by the presence of mobile DNA elements within the genome

Benedetta Orfei; Joël F Pothier; Linda Fenske; Jochen Blom; Chiaraluce Moretti; Roberto Buonaurio; Theo H M Smits

doi:10.3389/fpls.2023.1197706

Race-specific genotypes of Pseudomonas syringae pv. tomato are defined by the presence of mobile DNA elements within the genome

Front Plant Sci. 2023 Jul 5:14:1197706. doi: 10.3389/fpls.2023.1197706. eCollection 2023.

Authors

Benedetta Orfei¹, Joël F Pothier², Linda Fenske³, Jochen Blom³, Chiaraluce Moretti¹, Roberto Buonaurio¹, Theo H M Smits²

Affiliations

¹ Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy.
² Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.
³ Bioinformatics and Systems Biology, Justus-Liebig University Giessen, Giessen, Germany.

Abstract

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck of tomato, an important disease that results in severe crop production losses worldwide. Currently, two races within phylogroup 01a (PG01a) are described for this pathogen. Race 0 strains have avirulence genes for the expression of type III system-associated effectors AvrPto1 and AvrPtoB, that are recognized and targeted by the effector-triggered immunity in tomato cultivars having the pto race-specific resistance gene. Race 1 strains instead lack the avrPto1 and avrPtoB genes and are therefore capable to aggressively attack all tomato cultivars. Here, we have performed the complete genome sequencing and the analysis of P. syringae pv. tomato strain DAPP-PG 215, which was described as a race 0 strain in 1996. Our analysis revealed that its genome comprises a 6.2 Mb circular chromosome and two plasmids (107 kb and 81 kb). The results indicate that the strain is phylogenetically closely related to strains Max13, K40, T1 and NYS-T1, all known race 1 strains. The chromosome of DAPP-PG 215 encodes race 1-associated genes like avrA and hopW1 and lacks race 0-associated genes like hopN1, giving it a race 1 genetic background. However, the genome harbors a complete ortholog of avrPto1, which allows the strain to display a race 0 phenotype. Comparative genomics with several PG01a genomes revealed that mobile DNA elements are rather involved in the evolution of the two different races.

Keywords: AvrPto1; AvrPtoB; Pseudomonas avellanae; Pseudomonas syringae pv. tomato; comparative genomics; race shift.

Grants and funding

JP and TS were supported by the Department of Life Sciences and Facility Management of the Zurich University of Applied Sciences (ZHAW) in Wädenswil. The EDGAR platform is funded by the BMBF grant FKZ031A533 within the de.NBI network. CM and RB were supported by the research fund “Ricerca di Base” of Department of Agricultural, Food and Environmental Sciences (DSA3) of the University of Perugia, Italy.