An acquisition account of genomic islands based on genome signature comparisons.
BACKGROUND
Recent 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.


RESULTS
Of 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.


CONCLUSIONS
From 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.
van Passel
M W J
MW
Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands. m.w.vanpassel@amc.uva.nl
Bart
A
A
Thygesen
H H
HH
Luyf
A C M
AC
van Kampen
A H C
AH
van der Ende
A
A
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping; D002875:Chromosomes; D002876:Chromosomes, Bacterial; D016000:Cluster Analysis; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D018014:Gene Transfer Techniques; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D008040:Genetic Linkage; D016678:Genome; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics; D010957:Plasmids; D017422:Sequence Analysis, DNA; D041261:Vibrio vulnificus / Q000235:genetics*