Coleman, M. L. 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: 31.48). 04/2006; 311(5768):1768-70. DOI: 10.1126/science.1122050
Source: PubMed

ABSTRACT 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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    • "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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    • "However, inferring function based on the 16S rRNA gene is only possible in selected cases where all members of a 16S-defined clade share the same physiology, e.g., in case of cyanobacteria or certain groups of sulfate-reducing Deltaproteobacteria. Further, various studies have demonstrated substantial genomic variations among strains that differ only slightly in 16S rRNA sequences (Coleman et al., 2006; Rasko et al., 2008; Tettelin et al., 2008). Therefore, a genome-scale understanding of how genes evolve and what determines the acquisition and deletion of genes is essential for mapping the complete genetic variations of bacteria, while at the same time assisting in the classification and functional identification of bacterial species. "
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    • "These regions have been named metagenomic islands (MGIs) and overlap mostly (but not completely) with the flexible genome (defined when comparing different strain genomes) (Coleman et al., 2006; Cuadros-Orellana et al., 2007; Paši´c et al., 2009). Overall, these data can be explained by a high degree of concurrent genomic diversity in prokaryotic populations (Gonzaga et al., 2012; López-Pérez et al., 2013). "
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