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

Abstract

<div><p>The European hazelnut (<i>Corylus avellana</i>) 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 <i>Pseudomonas</i> strains isolated from symptomatic <i>C</i>. <i>avellana</i> trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: <i>P</i>. <i>avellanae</i> and <i>P</i>. <i>syringae</i>. The latter including the pathovars <i>avellanae</i>, <i>coryli</i> and <i>syringae</i>. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the <i>hrp/hrc</i> 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 <i>P</i>. <i>avellanae</i> showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all <i>P</i>. <i>syringae</i> pathovar strains, whereas the siderophore yersiniabactin was only present in <i>P</i>. <i>avellanae</i>. 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 <i>Pseudomonas</i> 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.</p></div