Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits

Abstract

The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches.

Extensive Field Survey, Laboratory and Greenhouse Studies Reveal Complex Nature of Pseudomonas syringae-Associated Hazelnut Decline in Central Italy

“…MLST sequences of the Pav strains isolated previously from Greece and Italy were reported by Wang et al [ 18 ]. Sequences for PavCRAFRUec1, PavCRAFRUec2 and PavCRAFRUec3 are published by Marcelletti and Scortichini [ 41 ]. Pseudomonas aeruginona (PAO1) was used as an outgroup.…”

“…syringae phylogroup 1 while strains isolated in Italy belonged to the phylogroup 2 of P . syringae [ 18 , 41 ]. Further studies based on comparative genomics also hypothesized that the two phylogenetic P .…”

“…Further studies based on comparative genomics also hypothesized that the two phylogenetic P . syringae lines experienced a convergent evolution that led to a similar pathogenic phenotype on hazelnut plants [ 19 , 41 ]. However, here we demonstrate that only the phylogroup 1 strains of P .…”

Divorcing Strain Classification From Species Names

“…Strains within the group P. syringae were first categorized and split up into nine different genomospecies based upon DNA-DNA hybridization [24]. Later, strains were classified into 13 different groups by multilocus sequence type ( MLST) and multiple subgroups, with a reduced yet accurate scheme including the loci rpoD, gltA, cit , and gyrB [28,29], Whole genome phylogenies can now be built using a variety of methods and with draft genomes, all approximate the earlier classification schemes (although there are notable exceptions) [30-32]. Given the current state of the field, one can reasonably determine where within P, syringae sensu lato their strains of interest fall given a sequence for only the gltA locus (Figure 1 and [28]).…”

A Volatile Signal Controls Virulence in the Plant PathogenPseudomonas syringaepv.syringaeand a Strategy for Infection Control in Organic Farming

“…14 The mbo gene cluster encoding the mangotoxin biosynthesis genes was first described in Pss 16 and was later also identified in many other P. syringae pathovars. [17][18][19] Investigations of the regulation of mangotoxin production has led to the identification of the mgo operon, which was shown to be required for the production of an unknown signal molecule. 20,21 The mgo gene cluster comprises four genes, namely mgoB, a predicted haem oxygenase, mgoC, a homolog of the N-oxygenase aurF, 22 mgoA, a non-ribosomal peptide synthetase (NRPS) and mgoD a putative polyketide cyclase/dehydratase.…”