Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle.

Boris Alexander Vinatzer,Pedro Manuel Martínez-García,Francisco M Cazorla,José Antonio Gutiérrez-Barranquero,Alejandro Pérez-García,Cayo Ramos,Antonio De Vicente,Eva Arrebola,Víctor J Carrión,Pablo Rodríguez-Palenzuela

doi:10.1371/journal.pone.0136101

Abstract

The genome sequence of more than 100 Pseudomonas syringae strains has been sequenced to date; however only few of them have been fully assembled, including P. syringae pv. syringae B728a. Different strains of pv. syringae cause different diseases and have different host specificities; so, UMAF0158 is a P. syringae pv. syringae strain related to B728a but instead of being a bean pathogen it causes apical necrosis of mango trees, and the two strains belong to different phylotypes of pv.syringae and clades of P. syringae. In this study we report the complete sequence and annotation of P. syringae pv. syringae UMAF0158 chromosome and plasmid pPSS158. A comparative analysis with the available sequenced genomes of other 25 P. syringae strains, both closed (the reference genomes DC3000, 1448A and B728a) and draft genomes was performed. The 5.8 Mb UMAF0158 chromosome has 59.3% GC content and comprises 5017 predicted protein-coding genes. Bioinformatics analysis revealed the presence of genes potentially implicated in the virulence and epiphytic fitness of this strain. We identified several genetic features, which are absent in B728a, that may explain the ability of UMAF0158 to colonize and infect mango trees: the mangotoxin biosynthetic operon mbo, a gene cluster for cellulose production, two different type III and two type VI secretion systems, and a particular T3SS effector repertoire. A mutant strain defective in the rhizobial-like T3SS Rhc showed no differences compared to wild-type during its interaction with host and non-host plants and worms. Here we report the first complete sequence of the chromosome of a pv. syringae strain pathogenic to a woody plant host. Our data also shed light on the genetic factors that possibly determine the pathogenic and epiphytic lifestyle of UMAF0158. This work provides the basis for further analysis on specific mechanisms that enable this strain to infect woody plants and for the functional analysis of host specificity in the P. syringae complex.

Highlights

Pseudomonas syringae is a species of Gram-negative plant pathogenic bacteria that cause disease in many agriculturally important crops [1]
The P. syringae pv. syringae UMAF0158 genome is composed of one circular chromosome of 5787986 bp (Table 1; Fig 1) and one plasmid
Among the predicted chromosomal coding sequences (CDSs), a putative function was assigned to 4030 (80%), while the remaining 987 CDSs were designated as hypothetical proteins

Summary

Introduction

Pseudomonas syringae is a species of Gram-negative plant pathogenic bacteria that cause disease in many agriculturally important crops [1]. Based on plant pathogenicity test and host specificity, strains belonging to the P. syringae complex are subdivided into 57 pathovars [3]. DNA hybridization segregated the P. syringae complex into at least nine different genomospecies [4,5] and multilocus sequence typing (MLST) permitted the classification into 13 phylogroups, including 23 differentiated clades [6]. Many pathovars associated with unrelated plants are grouped together, sometimes even within the same clade [6]. P. syringae is an ideal system to study how evolutionary forces shape adaptation to different hosts, which makes it an archetype of plant-pathogen interactions [7,10]

Methods

Results

Conclusion