Coleman ML, Sullivan MB, Martiny AC, Steglich C, Barry K, DeLong EF et al.. Genomic Islands and the ecology and evolution of Prochlorococcus. Science 311: 1768-1770

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
Science (Impact Factor: 33.61). 04/2006; 311(5768):1768-70. DOI: 10.1126/science.1122050
Source: PubMed


Prochlorococcus ecotypes are a useful system for exploring the origin and function of diversity among closely related microbes. The genetic variability between phenotypically distinct strains that differ by less that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands. Island genes appear to have been acquired in part by phage-mediated lateral gene transfer, and some are differentially expressed under light and nutrient stress. Furthermore, genome fragments directly recovered from ocean ecosystems indicate that these islands are variable among cooccurring Prochlorococcus cells. Genomic islands in this free-living photoautotroph share features with pathogenicity islands of parasitic bacteria, suggesting a general mechanism for niche differentiation in microbial species.

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    • "These regions have been termed metagenomic islands to distinguish them from genomic islands identified by comparison of closely related strains [26], although there appears to be a considerable overlap in function of the genes encoded in both types of island. Coleman et al. [28] were the first to align metagenomic sequences against a set of completely sequenced strains of Prochlorococcus marinus and to report the existence of metagenomic islands. This strategy was coined " genome recruitment analysis " . "
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    • "To better identify regions that have been transferred in vent genomes, we compared genomes from bacterial or archaeal isolates with sequences sampled directly from the environment. This strategy can identify potential hypervariable regions, or “genomic islands,” that display lower coverage than the rest of the genome [47]–[49]. Previous work with Haloquadratum walsbyi DSM 16790 [48] and Prochlorococcus genomes [47] used this technique to identify genomic islands that most likely represented regions of virally-mediated lateral gene transfer; in the case of Prochlorococcus, these genes are differentially expressed under light and nutrient stress [47]. "
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    • "In the Prochlorococcus-virus system, host resistance-associated mutations seem confined to a hyper-variable region, known to be associated with viral attachment to the host cell surface and are linked with a fitness cost to the host (Avrani et al., 2011). Moreover, most genes found in genomic islands result from horizontal gene transfer and/ or recombination events (Coleman et al., 2006; Lindell et al., 2007). The newly identified hyper-variable region in the EhV genome could also represent a hotspot for those events. "
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