IslandViewer: an integrated interface for computational identification and visualization of genomic islands

Langille, Morgan G. I.; Brinkman, Fiona S. L.

doi:10.1093/bioinformatics/btp030

Cited by 359 publications

(369 citation statements)

References 15 publications

(14 reference statements)

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“…However, we obtained more mobile GIs than ones identified by Islander. GIs found by IslandViewer did not contain flanking direct sequences compared with our results [20]. Mathee et al [21] identified more GI regions in P. aeruginosa PAO1 and PA14 than the current study, but did not accurately localize these GIs.…”

Section: Discussioncontrasting

confidence: 85%

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Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

Song

Zhang

2011

Chin. Sci. Bull.

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Mobile genomic islands (GIs) can be excised from the chromosome, then form a circular intermediate and be reintegrated into the chromosome by the GI internal integrase. Some mobile GIs can also be transferred into a new receptor cell by transformation, conjugation, or transduction. The action sites of the integrase are usually flanked direct repeats (DRs) of the GIs. Accurate localization of the flanking sequences is a precondition for determining the mobility of the GI. Mobile GIs are generally associated with transfer RNAs (tRNAs). Based on the correlation between flanking sequences and tRNA sequences, the flanking sequences of 11 putative mobile GIs in Pseudomonas aeruginosa PAO1, P. aeruginosa PA14, P. fluorescens Pf-5 and P. fluorescens Pf0-1 were identified. Among the 11 GIs, Pf0-1GI-1 is responsible for benzoate degradation. PAO1GI-1, Pf5GI-2, Pf5GI-3, and Pf5GI-4 were confirmed experimentally to be excised from a chromosome to form a circular intermediate. The action sites of the integrases are these GIs direct repeats. Due to distinct DRs, cutting sites for the internal integrase of PAO1GI-1, Pf5GI-2, Pf5GI-3 and Pf5GI-4 were determined outside the T-loop of the tRNA Gly gene, outside the anticodon loop of the tRNA Ser gene and tRNALys gene, and at the asymmetric 3′-end of the tRNA Leu gene, respectively. PAO1GI-1 and other mobile GIs may be transferred into many different strains that belong to different phyla because of the clear flanking sequences. This study describes basic information about the action sites of the integrases, assesses the mobility of GIs, and can help design and transfer mobile GIs to candidate strains. Pseudomonas, genomic islands, accurate localization, excision, integraseCitation: Song L, Zhang X H. Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens.

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Section: Discussioncontrasting

confidence: 85%

“…The genomic location of six GIs in P. aeruginosa was identical to those in our previous report [18], but their mobility was not determined. A number of studies have also described the regions of GIs in these four strains [14,[19][20][21][22][23]. These data have been presented in comparison with the 11 GIs of the present study ( Table 4).…”

Section: Discussionmentioning

confidence: 55%

Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

Song

Zhang

2011

Chin. Sci. Bull.

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“…This cut-off value will allow hits from 100 % coverage with up to 80 % identities to 80 % coverage with 100 % identities. Genomic islands were identified for spacer hits with an IC score above the cut-off using SIGI-HMM (Waack et al, 2006), IslandPath (Hsiao et al, 2003) and IslandPick (Langille et al, 2008) as implemented in the IslandViewer (Langille & Brinkman, 2009) and the prophage sequences were identified using PHAST (Zhou et al, 2011).…”

Section: Methodsmentioning

confidence: 99%

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

2013

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Clustered regularly interspaced short palindromic repeats (CRISPRs) are major barriers to recombination through recognition of invading nucleic acids, such as phage and plasmids, and promoting their degredation through the action of CRISPR associated (Cas) proteins. The genomic comparison of 17 Corynebacterium diphtheriae strains led to the identification of three novel CRISPR-Cas system variants, based on the Type II (Type II-C) or type I-E systems. The type II-C system was the most common (11/17 isolates) but it lacked the csn2 and cas4 genes that are involved in spacer acquisition. We also identified that this variant type II-C CRISPR-Cas system is present in other bacteria, and the first system was recently characterized in Neisseria meningitidis. In the remaining isolates, the type II-C system was replaced by a variant of type I-E (I-E-a), where the repeat arrays are inserted between the cas3 and cse1 genes. Three isolates with the type II-C system also possess an additional variant of type I-E (I-E-b), elsewhere in the genome, that exhibits a novel divergent gene organization within the cas operon. The nucleotide sequences of the palindromic repeats and the cas1 gene were phylogenetically incongruent to the core genome. The G+C content of the systems is lower (46.0-49.5 mol%) than the overall DNA G+C content (53 mol%), and they are flanked by mobile genetic elements, providing evidence that they were acquired in three independent horizontal gene transfer events. The majority of spacers lack identity with known phage or plasmid sequences, indicating that there is an unexplored reservoir of corynebacteriophages and plasmids. These novel CRISPR-Cas systems may represent a unique mechanism for spacer acquisitions and defence against invading DNA.

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“…MED134, L. blandensis MED217 and 'G. forsetii' KT0803 were extracted (Fernández-Gó mez et al, 2012) using IslandViewer database for identification and visualization of GIs (Langille and Brinkman, 2009;Langille et al, 2010).…”

Section: Gene Prediction and Annotationmentioning

confidence: 99%

Ecology of marine Bacteroidetes: a comparative genomics approach

et al. 2013

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Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO 2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface.

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IslandViewer: an integrated interface for computational identification and visualization of genomic islands

Cited by 359 publications

References 15 publications

Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

Ecology of marine Bacteroidetes: a comparative genomics approach

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