Identification of genomic islands in six plant pathogens

Chen, Ling-Ling

doi:10.1016/j.gene.2006.01.029

Cited by 14 publications

(14 citation statements)

References 27 publications

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“…The homogeneity of G+C content of a GI is one feature only mentioned and employed by Zhang and colleagues (Chen, 2006;Zhang and Zhang, 2004a,b, 2005Wei and Guo, 2011;. According to them, GIs usually have fairly constant G+C content, and hence, they show almost straight lines in the cumulative GC profile.…”

Section: H Index Of Gi Homogeneitymentioning

confidence: 99%

“…Besides the above frequently-mentioned features of GIs, we also wanted to investigate one relatively new feature, which has been used as one of the standards for predicting novel GIs by Zhang and colleagues (Chen, 2006;Zhang and Zhang, 2004a,b, 2005Wei and Guo, 2011;. The homogeneity feature was obtained based on the cumulative GC profile (Zhang et al, 2001).…”

Section: Cumulative Gc Profile and H Indexmentioning

confidence: 99%

“…The homogeneity feature was obtained based on the cumulative GC profile (Zhang et al, 2001). The method of the cumulative GC profile proposed by Zhang and colleagues has been used to identify GIs in dozens of prokaryotic genomes (Charkowski, 2004;Greub et al, 2004;Chen, 2006;Do and Miyano, 2008;Zhang and Zhang, 2004a,b, 2005Wei and Guo, 2011). The method is described briefly as follows.…”

Section: Cumulative Gc Profile and H Indexmentioning

confidence: 99%

“…GIs usually have a fairly homogeneous GC content, and this fact could be reflected by the corresponding Z' curve being a nearly straight line (Guo et al, 2003;Charkowski, 2004;Greub et al, 2004;Chen, 2006;Do and Miyano, 2008;Zhang and Zhang, 2004a,b, 2005Wei and Guo, 2011). An index called h (Zhang and Zhang, 2004b), which quantitatively describes the homogeneity of the GC content of a GI, is defined by the following equation,…”

Section: Cumulative Gc Profile and H Indexmentioning

confidence: 99%

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Statistical analyses of conserved features of genomic islands in bacteria

Guo¹,

Xia²,

Wang³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. We performed statistical analyses of five conserved features of genomic islands of bacteria. Analyses were made based on 104 known genomic islands, which were identified by comparative methods. Four of these features include sequence size, abnormal G+C content, flanking tRNA gene, and embedded mobility gene, which are frequently investigated. One relatively new feature, G+C homogeneity, was also investigated. Among the 104 known genomic islands, 88.5% were found to fall in the typical length of 10-200 kb and 80.8% had G+C deviations with absolute values larger than 2%. For the 88 genomic islands whose hosts have been sequenced and annotated, 52.3% of them were found to have flanking tRNA genes and 64.7% had embedded mobility genes. For the homogeneity feature, 85% had an h homogeneity index less than 0.1, indicating that their G+C content is relatively uniform. Taking all the five features into account, 87.5% of 88 genomic islands had three of them. Only one genomic island had only one conserved feature and none of the genomic islands had zero features. These statistical results should help to understand the general structure of known genomic islands. We found that larger genomic islands tend to have relatively small G+C deviations relative to absolute values. For example, the absolute G+C deviations of 9 genomic islands longer than 100,000 bp were all less than 5%. This is a Feature analyses of bacterial genomic islands novel but reasonable result given that larger genomic islands should have greater restrictions in their G+C contents, in order to maintain the stable G+C content of the recipient genome.

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Section: H Index Of Gi Homogeneitymentioning

confidence: 99%

Section: Cumulative Gc Profile and H Indexmentioning

confidence: 99%

Section: Cumulative Gc Profile and H Indexmentioning

confidence: 99%

Section: Cumulative Gc Profile and H Indexmentioning

confidence: 99%

See 2 more Smart Citations

Statistical analyses of conserved features of genomic islands in bacteria

Guo¹,

Xia²,

Wang³

et al. 2014

Genet. Mol. Res.

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“…Interestingly, these same pathogenicity systems are also used by plant pathogens (e.g. Erwinia, Pseudomonas, Xanthomonas and Ralstonia) to infect numerous agriculturally important plants (Chen, 2006;Shumann, 1991;van der Zwet & Beer, 1995), sometimes leading to millions of US dollars worth of losses each year among certain agricultural commodities.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens

2009

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This study uses sequences from four genes, which are involved in the formation of the type III secretion apparatus, to determine the role of horizontal gene transfer in the evolution of virulence genes for the enterobacterial plant pathogens. Sequences of Erwinia, Brenneria, Pectobacterium, Dickeya and Pantoea were compared (a) with one another, (b) with sequences of enterobacterial animal pathogens, and (c) with sequences of plant pathogenic c and b proteobacteria, to evaluate probable paths of lateral exchange leading to the current distribution of virulence determinants among these micro-organisms. Phylogenies were reconstructed based on hrcC, hrcR, hrcJ and hrcV gene sequences using parsimony and maximum-likelihood algorithms. Virulence gene phylogenies were also compared with several housekeeping gene loci in order to evaluate patterns of lateral versus vertical acquisition. The resulting phylogenies suggest that multiple horizontal gene transfer events have occurred both within and among the enterobacterial plant pathogens and plant pathogenic c and b proteobacteria. hrcJ sequences are the most similar, exhibiting anywhere from 2 to 50 % variation at the nucleotide level, with the highest degree of variation present between plant and animal pathogen sequences. hrcV sequences are conserved among plant and animal pathogens at the N terminus. The C-terminal domain is conserved only among the enterobacterial plant pathogens, as are the hrcC and hrcR sequences. Additionally, hrcJ and hrcV sequence phylogenies suggest that at least some type III secretion system virulence genes from enterobacterial plant pathogens are related more closely to those of the genus Pseudomonas, a conclusion neither supported nor refuted by hrcC or hrcR.

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