Identification of genomic islands in six plant pathogens.
Genomic islands (GIs) play important roles in microbial evolution, which are acquired by horizontal gene transfer. In this paper, the GIs of six completely sequenced plant pathogens are identified using a windowless method based on Z curve representation of DNA sequences. Consequently, four, eight, four, one, two and four GIs are recognized with the length greater than 20-Kb in plant pathogens Agrobacterium tumefaciens str. C58, Rolstonia solanacearum GMI1000, Xanthomonas axonopodis pv. citri str. 306 (Xac), Xanthomonas campestris pv. campestris str. ATCC33913 (Xcc), Xylella fastidiosa 9a5c and Pseudomonas syringae pv. tomato str. DC3000, respectively. Most of these regions share a set of conserved features of GIs, including an abrupt change in GC content compared with that of the rest of the genome, the existence of integrase genes at the junction, the use of tRNA as the integration sites, the presence of genetic mobility genes, the difference of codon usage, codon preference and amino acid usage, etc. The identification of these GIs will benefit the research for the six important phytopathogens.
Chen
Ling-Ling
LL
Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China. llchen@sdut.edu.cn
D016960:Agrobacterium tumefaciens / Q000235:genetics / Q000472:pathogenicity; D001482:Base Composition / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands / Q000235:genetics*; D006090:Gram-Negative Bacteria / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity*; D010944:Plants / Q000382:microbiology*; D044224:Pseudomonas syringae / Q000235:genetics / Q000472:pathogenicity; D043368:Ralstonia solanacearum / Q000235:genetics / Q000472:pathogenicity; D017422:Sequence Analysis, DNA; D014974:Xanthomonas / Q000235:genetics / Q000472:pathogenicity; D016959:Xanthomonas campestris / Q000235:genetics / Q000472:pathogenicity; D044167:Xylella / Q000235:genetics / Q000472:pathogenicity
D004269:DNA, Bacterial