PPI logo P. s. pv. tomato DC3000 P. s. pv. phaseolicola 1448A
Comparative Genomics and Genome Organization

genome resources
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Genome comparison resources for Pseudomonas syringae:

Lindeberg et al, 2008. Roadmap to new virulence determinants in Pseudomonas syringae: Insights from comparative genomics and genome organization. MPMI 21:685-700.
thumbnail shown:
loci PSPTO_0800-0900

"BLAST fingerprint" showing representation of Pto DC3000 coding sequences in 58 other genera as determined by BLASTP analysis.  Orthology of Pto DC3000 loci (shown in sequential order on the x-axis) with orfs in selected bacterial genomes (listed on the y-axis) is indicated with colored squares, with intensity of color is proportional to the degree of sequence similarity:

hyperlinked thumbnail images for all Pto DC3000 loci
figure legend with list of genomes compared


Genome comparison wheel showing representation of P. syringae pv. tomato DC3000 coding sequences (outermost ring) in selected bacterial genomes (inner rings) as determined by BLASTP analysis:

Powerpoint image
figure legend with list of genomes compared

View variable regions using the Artemis genome viewer - Pto DC3000 variable regions tab file (more about using Artemis)
Table 2 - Locations of virulence and host-association factors relative to the variable genome regions, identified by analysis of compositional deviation and sequence alignment of the Pto DC3000, Pph 1448A, and Psy B728a genomes
Table 3 - List of variable regions in the Pto DC3000, Pph 1448a, and Psy B728a genomes showing the basis for their identification, size and for Pto DC3000, variable region loci, presence of mobile genetic elements (MGEs), and presence of tRNAs [Excel file - Sheet 1]
Table 4 - Representation and syntenic conservation of virulence and host-association genes among the Pto DC3000, Pph 1448a, and Psy B728a genomes [Excel file - Sheet 2]
Table 5 - Pto DC3000 genes with orthologs in no more than two of the 41 bacterial genomes screened as determined by BLASTP analysis
[Excel file - Sheet 3]

Additional publications containing Pseudomonas syringae genome comparison data:

Feil, et al, 2005. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc. Natl. Acad. Sci 102:11064-11069.

Joardar, et al, 2005. Whole-Genome Sequence Analysis of Pseudomonas syringae pv.phaseolicola 1448A Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition J. Bacteriol. 187:6488-98.

Joardar, et al. 2005. Lineage-specific regions in Pseudomonas syringae pv. tomato DC3000. Mol. Plant Path. 6:53 [comparison of Pto DC3000 genomes with those of P putida and P. aeruginosa PAO1]







Magdalen Lindeberg
PPI Project Coordinator
Plant Pathology and Plant-Microbe Biology
Cornell University