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Open Access Highly Accessed Research article

Patterns and architecture of genomic islands in marine bacteria

Beatriz Fernández-Gómez1, Antonio Fernàndez-Guerra2, Emilio O Casamayor2, José M González3, Carlos Pedrós-Alió1 and Silvia G Acinas1*

Author Affiliations

1 Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Pg Marítim de la Barceloneta 37-49, ES-08003, Barcelona, Spain

2 Biogeodynamics & Biodiversity Group, Centre d'Estudis Avançats de Blanes, CEAB-CSIC, ES-17300, Blanes, Spain

3 Department of Microbiology, University of La Laguna, ES-38206 La Laguna, Tenerife, Spain

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BMC Genomics 2012, 13:347  doi:10.1186/1471-2164-13-347

Published: 29 July 2012

Abstract

Background

Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial genomes have not been explored systematically to uncover possible trends and to analyze their putative ecological significance.

Results

We carried out a comprehensive analysis of GIs in 70 selected marine bacterial genomes detected with IslandViewer to explore the distribution, patterns and functional gene content in these genomic regions. We detected 438 GIs containing a total of 8152 genes. GI number per genome was strongly and positively correlated with the total GI size. In 50% of the genomes analyzed the GIs accounted for approximately 3% of the genome length, with a maximum of 12%. Interestingly, we found transposases particularly enriched within Alphaproteobacteria GIs, and site-specific recombinases in Gammaproteobacteria GIs. We described specific Homologous Recombination GIs (HR-GIs) in several genera of marine Bacteroidetes and in Shewanella strains among others. In these HR-GIs, we recurrently found conserved genes such as the β-subunit of DNA-directed RNA polymerase, regulatory sigma factors, the elongation factor Tu and ribosomal protein genes typically associated with the core genome.

Conclusions

Our results indicate that horizontal gene transfer mediated by phages, plasmids and other mobile genetic elements, and HR by site-specific recombinases play important roles in the mobility of clusters of genes between taxa and within closely related genomes, modulating the flexible pool of the genome. Our findings suggest that GIs may increase bacterial fitness under environmental changing conditions by acquiring novel foreign genes and/or modifying gene transcription and/or transduction.

Keywords:
Genomic islands; Horizontal gene transfer; Homologous recombination; Bacterial core genes; Flexible genome; Structure of genomic islands; Patterns within genomic islands; Marine bacteria