ArticleBMC genomics2005
An acquisition account of genomic islands based on genome signature comparisons.
Article in BMC genomics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Genomic Signature in Evolutionary Biology: A Review.Biology · 2023Review
- Symbiosis genes show a unique pattern of introgression and selection within aMicrobial genomics · 2020Article
- The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes.BMC genomics · 2017Article
- Meningococcal Two-Partner Secretion Systems and Their Association with Outcome in Patients with Meningitis.Infection and immunity · 2016Article
- Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.Database : the journal of biological databases and curation · 2015Article
- Tracing common origins of Genomic Islands in prokaryotes based on genome signature analyses.Mobile genetic elements · 2011Article
- A quantitative account of genomic island acquisitions in prokaryotes.BMC genomics · 2011Article
- The mosaicism of plasmids revealed by atypical genes detection and analysis.BMC genomics · 2011Article
- The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination.Virology journal · 2010Article
- Article
- Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus.BMC genomics · 2010Article
- A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes.Genome biology · 2009Article
- Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes.Nucleic acids research · 2008Article
- Molecular characterization of cold adaptation based on ortholog protein sequences from Vibrionaceae species.Extremophiles : life under extreme conditions · 2007Article
- The reach of the genome signature in prokaryotes.BMC evolutionary biology · 2006Article
- Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.BMC genomics · 2006Article
- Viral metagenomics.Reviews in medical virologyReview
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent analyses of prokaryotic genome sequences have demonstrated the important force horizontal gene transfer constitutes in genome evolution. Horizontally acquired sequences are detectable by, among others, their dinucleotide composition (genome signature) dissimilarity with the host genome. Genomic islands (GIs) comprise important and interesting horizontally transferred sequences, but information about acquisition events or relatedness between GIs is scarce. In Vibrio vulnificus CMCP6, 10 and 11 GIs have previously been identified in the sequenced chromosomes I and II, respectively. We assessed the compositional similarity and putative acquisition account of these GIs using the genome signature. For this analysis we developed a new algorithm, available as a web application.
resultsOf 21 GIs, VvI-1 and VvI-10 of chromosome I have similar genome signatures, and while artificially divided due to a linear annotation, they are adjacent on the circular chromosome and therefore comprise one GI. Similarly, GIs VvI-3 and VvI-4 of chromosome I together with the region between these two islands are compositionally similar, suggesting that they form one GI (making a total of 19 GIs in chromosome I + chromosome II). Cluster analysis assigned the 19 GIs to 11 different branches above our conservative threshold. This suggests a limited number of compositionally similar donors or intragenomic dispersion of ancestral acquisitions. Furthermore, 2 GIs of chromosome II cluster with chromosome I, while none of the 19 GIs group with chromosome II, suggesting an unidirectional dispersal of large anomalous gene clusters from chromosome I to chromosome II.
conclusionFrom the results, we infer 10 compositionally dissimilar donors for 19 GIs in the V. vulnificus CMCP6 genome, including chromosome I donating to chromosome II. This suggests multiple transfer events from individual donor types or from donors with similar genome signatures. Applied to other prokaryotes, this approach may elucidate the acquisition account in their genome sequences, and facilitate donor identification of GIs.
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