Genomic Characterization of Pseudomonas syringae pv. syringae Populations Affecting Sweet Cherry Orchards in Chile Reveals Local Adaptation and Virulence Signatures

TL;DR

This study explores the genetic diversity of a bacterial pathogen affecting sweet cherry trees in Chile, revealing local adaptation and virulence traits.

Contribution

The study identifies unique genomic features and lineage-specific adaptations in Chilean Pss populations.

Findings

Chilean Pss isolates predominantly belong to the PG2d subgroup with 18 genomic clusters.

The PG2d subgroup has IAA synthesis genes and shows extensive genomic remodeling.

Copper resistance and T6SS systems were found in some strains, indicating adaptive evolution.

Abstract

Pseudomonas syringae pv. syringae (Pss) is an economically significant bacterial pathogen that causes canker in sweet cherry trees. In Chile, sweet cherry (Prunus avium L.) is a key crop whose exponential production growth has increased phytosanitary pressure. However, the genetic diversity and adaptive mechanisms of local Pss populations have remained poorly understood. This study characterized 41 Pss isolates from major Chilean production regions. Their genomes were sequenced and compared with 152 public genomes from the PG2 phylogenetic group. The analysis revealed a predominance of the PG2d subgroup among the Chilean isolates, with a population structure defined by at least 18 genomic clusters, some of which are exclusive to Chile. A characteristic feature of this entire PG2d subgroup is the presence of indole-3-acetic acid (IAA) synthesis genes (iaaM and iaaH). Furthermore, this subgroup displayed a marked increase in ancestral gene gain and loss events, indicating extensive remodeling of the shell genome and supporting a model of lineage-specific adaptive evolution. We also identified lineage-specific orthogroups, structural variants of the T-PAI pathogenicity island, and a differential distribution of Hop-type effector proteins. Furthermore, an extended copper resistance operon (cop and cus systems) was detected in a subset of strains, and a dominant lineage was found to have a dual i1-type of T6SS system. These findings highlight the local diversification of Pss in Chile, likely driven by agro-environmental pressures. This study provides crucial insights into the evolution, adaptation, and pathogenic potential of this important pathogen in a crop of high strategic value.

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