The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000

doi:10.1073/pnas.1731982100

The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000

^*The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850; ^‡Department of Plant Pathology, Cornell University, Ithaca, NY 14853; ^§Boyce Thompson Institute for Plant Research, Ithaca, NY 14853-1801; ^¶Plant Science Initiative and Department of Plant Pathology, University of Nebraska, Lincoln, NE 68588-0660; ^∥United States Department of Agriculture Agricultural Research Service, Cornell Theory Center, Ithaca, NY 14853-2901; ^**Department of Plant Microbiology and Pathology, University of Missouri, Columbia, MO 65211; ^††Department of Plant Pathology, Kansas State University, Manhattan, KS 66502-5502; and ^‡‡Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078

Edited by Robert Haselkorn, University of Chicago, Chicago, IL, and approved June 23, 2003 (received for review April 4, 2003)

Abstract

We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function.

Footnotes

↵ † To whom correspondence should be addressed. E-mail: rbuell{at}tigr.org.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: CMA, coronamic acid; COR, coronatine; DC3000, Pseudomonas syringae pv. tomato DC3000; GABA, γ-aminobutyric acid; IS, insertion sequence; Tfp, type IV pili; TTSS, type III secretion system.
Data deposition: The sequence and annotation of P. syringae pv. tomato DC3000 have been deposited in the GenBank database (accession nos. AE016853-AE016855).