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Comparative Study
. 2005 Aug 2;102(31):11064-9.
doi: 10.1073/pnas.0504930102. Epub 2005 Jul 25.

Comparison of the Complete Genome Sequences of Pseudomonas Syringae Pv. Syringae B728a and Pv. Tomato DC3000

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Free PMC article
Comparative Study

Comparison of the Complete Genome Sequences of Pseudomonas Syringae Pv. Syringae B728a and Pv. Tomato DC3000

Helene Feil et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

The complete genomic sequence of Pseudomonas syringae pv. syringae B728a (Pss B728a) has been determined and is compared with that of P. syringae pv. tomato DC3000 (Pst DC3000). The two pathovars of this economically important species of plant pathogenic bacteria differ in host range and other interactions with plants, with Pss having a more pronounced epiphytic stage of growth and higher abiotic stress tolerance and Pst DC3000 having a more pronounced apoplastic growth habitat. The Pss B728a genome (6.1 Mb) contains a circular chromosome and no plasmid, whereas the Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared with Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. Over 375 repetitive extragenic palindromic sequences unique to Pss B728a when compared with Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. Content of the genomic islands varies, with one containing a prophage and another the plasmid pKLC102 of Pseudomonas aeruginosa PAO1. Among the 976 genes of Pss B728a with no counterpart in Pst DC3000 are those encoding for syringopeptin, syringomycin, indole acetic acid biosynthesis, arginine degradation, and production of ice nuclei. The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to the epiphytic fitness and stress tolerance of this organism.

Figures

Fig. 1.
Fig. 1.
Chromosome of Pss B728a with the outermost circle depicting ORFs on the positive strand and the second circle depicting ORFs on the negative strand. The ORFs are color-coded based on the major grouping of role categories as follows: hypothetical proteins (black); conserved hypothetical proteins (light gray); nucleotide metabolism and transport (light red); translation, ribosomal structure, and biogenesis (yellow); signal transduction (lavender); transcription (magenta); lipid metabolism (cyan); carbohydrate metabolism and transport (blue); coenzyme metabolism (pink); energy metabolism (green); DNA replication, recombination, and repair (red); general function prediction (brown); cellular processes (sky blue); amino acid metabolism and transport (orange); and structural RNA (pale green). The third circle represents the ORFs with no orthologs in Pst DC3000 (E <10-5. The fourth circle represents the palindromic REPs color-coded as follows: family 1 (dark gray), family 2 (red), family 3 (green), family 4 (blue), family 5 (cyan), family 6 (magenta), family 7 (yellow), family 8 (pale green), family 9 (sky blue), family 10 (orange), family 11 (brown), and family 12 (light gray). The fifth and sixth circles represent GC content and skew respectively. The seventh and eighth circles represent the tRNA (green), rRNA (red), and misc_RNA (blue).
Fig. 2.
Fig. 2.
Comparison of chromosome structure for Pss B728a vs. Pst DC3000. Axes represent the portions coded for in the order in which they occur in the chromosomes. Top axis, B728a; bottom axis, DC3000. Red represents colinear regions on the + strand of both genomes, and blue represents colinear regions that have been inverted in one of the two genomes. The display was generated by using artemis comparison tool (ACT) (www.sanger.ac.uk/software/artemis/ACT).
Fig. 3.
Fig. 3.
Detailed view of the nonribosomal peptides and phytotoxins region of the Pss B728a genome. Comparison with the corresponding region for the Pst DC3000 is also shown.

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