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Front Microbiol. 2015 Aug 7;6:811. doi: 10.3389/fmicb.2015.00811. eCollection 2015.

Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea.

Author information

1
Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece.
2
Science and Technology Park of Sicily Catania, Italy.
3
School of Computing, Federal University of Mato Grosso do Sul Campo Grande, Brazil.
4
The Sainsbury Laboratory, John Innes Centre Norwich, UK.
5
Department of Agriculture, Food and Environment, University of Catania Catania, Italy.
6
Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece ; Plant Pathology and Bacteriology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece.
7
Centre for the Analysis of Genome Evolution & Function, University of Toronto Toronto, ON, Canada.
8
Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological Educational Institute of Crete Heraklion, Greece ; The Sainsbury Laboratory, John Innes Centre Norwich, UK.

Abstract

The non-fluorescent pseudomonads, Pseudomonas corrugata (Pcor) and P. mediterranea (Pmed), are closely related species that cause pith necrosis, a disease of tomato that causes severe crop losses. However, they also show strong antagonistic effects against economically important pathogens, demonstrating their potential for utilization as biological control agents. In addition, their metabolic versatility makes them attractive for the production of commercial biomolecules and bioremediation. An extensive comparative genomics study is required to dissect the mechanisms that Pcor and Pmed employ to cause disease, prevent disease caused by other pathogens, and to mine their genomes for genes that encode proteins involved in commercially important chemical pathways. Here, we present the draft genomes of nine Pcor and Pmed strains from different geographical locations. This analysis covered significant genetic heterogeneity and allowed in-depth genomic comparison. All examined strains were able to trigger symptoms in tomato plants but not all induced a hypersensitive-like response in Nicotiana benthamiana. Genome-mining revealed the absence of type III secretion system and known type III effector-encoding genes from all examined Pcor and Pmed strains. The lack of a type III secretion system appears to be unique among the plant pathogenic pseudomonads. Several gene clusters coding for type VI secretion system were detected in all genomes. Genome-mining also revealed the presence of gene clusters for biosynthesis of siderophores, polyketides, non-ribosomal peptides, and hydrogen cyanide. A highly conserved quorum sensing system was detected in all strains, although species specific differences were observed. Our study provides the basis for in-depth investigations regarding the molecular mechanisms underlying virulence strategies in the battle between plants and microbes.

KEYWORDS:

comparative genomics; effectors; non-ribosomal peptides; pith necrosis; polyketides; siderophores; type III secretion system; type VI secretion system

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