|Schneider, David - Dave|
|Buell, C. robin|
Submitted to: Molecular Plant Pathology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/4/2004
Publication Date: 1/8/2005
Citation: Joardar, V., Lindeberg, M., Schneider, D.J., Collmer, A., Buell, C. 2005. Lineage specific regions in pseudomonas syringae pv tomato dc3000. Molecular Plant Pathology. 6(1):53-64. Interpretive Summary: The genome for the plant pathogen, Pseudomonas syringae pv tomato DC3000 was compared to two closely related species, Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440 in order to identify lineage-specific regions - portions of the genome that are likely to be related to the specialization of P. syringae DC3000 as a plant pathogen, P. aeruginosa as an opportunistic human pathogen, and P. putida KT2440 as a non-pathogenic soil inhabitant. As expected, the comparison revealed large segments containing highly conserved genes related to essential metabolic functions. The portions of the DC3000 genome that are not shared with the other two species are also found in extended blocks that exhibit unique sequence "textures" that may be used to further distinguish these regions from the regions shared with one or both of the other species. More importantly, these lineage specific regions contain most of the previously known virulence-related genes, many genes of unknown function that may eventually be found to be related to virulence or host specificity, as well as many genes related to structural rearrangement of the genome itself. Because these lineage specific regions contain many uncharacterized genes that are closely associated with known virulence-related genes, they may be used by the research community to focus attention on a subsets of the genome that are likely to be involved in plant pathogenesis.
Technical Abstract: Comparative analyses of the chromosome of Pseudomonas syringae pv tomato DC3000 with the finished, complete genomes of Pseudomonas aeruginosa PAO1 and the Pseudomonas putida KT2440 revealed a high degree of sequence conservation in genes involved in "housekeeping functions". However, significant divergence is also observed making it possible to identify "suites" of species-specific genes which may provide the genetic basis for adaptation to an ecological niche and lifestyle. In particular, the DC3000 main chromosome contains 1,053 genes not present in either PAO1 or KT2440. The majority of these DC3000-specific genes either lack a known function or are mobile genetic elements. However, these genes do share features among themselves such as association with regions of atypical trinucleotides, unusual G+C content, and localization within large tracts of DC3000-specific sequence. These characteristics are suggestive of lateral gene transfer events. A comparison of syntenic blocks among these three complete genomes revealed that a substantial portion (533) of the DC3000-specific chromosomal genes (1053) were located in lineage-specific regions (defined as being larger than 2 kb and enriched in mobile genetic elements and/or genes specific to DC3000 in this three-way comparison). A large proportion of mobile genetic elements (62%) were located in such regions. Similarly, most of the genes encoding type III secretion system virulence effectors were located in lineage-specific regions. Finally, a putative chromosomal inversion mediated by identical copies of ISPsy6 involving nearly half of the DC3000 genome was detected.