title: Patterns and architecture of genomic islands in marine bacteria.
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.
authors: Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Pg Marítim de la Barceloneta 37-49, ES-08003 Barcelona, Spain.
authors: Beatriz
authors: B
authors: Fernández-Gómez
authors: Antonio
authors: A
authors: Fernàndez-Guerra
authors: Emilio O
authors: EO
authors: Casamayor
authors: José M
authors: JM
authors: González
authors: Carlos
authors: C
authors: Pedrós-Alió
authors: Silvia G
authors: SG
authors: Acinas
mesh_terms: D059001:Aquatic Organisms / Q000235:genetics; D001419:Bacteria / Q000235:genetics*; D030541:Databases, Genetic; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D014871:Water Microbiology