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BMC Genomics  2009 

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber

DOI: 10.1186/1471-2164-10-570

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Abstract:

Three regions of the sequenced isolate were scarcely represented in the metagenome thus appearing to vary among co-occurring S. ruber cells. These metagenomic islands showed evidence of extensive genomic corruption with atypically low GC content, low coding density, high numbers of pseudogenes and short hypothetical proteins. A detailed analysis of island gene content showed that the genes in metagenomic island 1 code for cell surface polysaccharides. The strain-specific genes of metagenomic island 2 were found to be involved in biosynthesis of cell wall polysaccharide components. Finally, metagenomic island 3 was rich in DNA related enzymes.The genomic organisation of S. ruber variable genomic regions showed a number of convergences with genomic islands of marine microbes studied, being largely involved in variable cell surface traits. This variation at the level of cell envelopes in an environment devoid of grazing pressure probably reflects a global strategy of bacteria to escape phage predation.Prokaryotic genomes are extraordinarily plastic entities and vary widely within the limits of a well defined species. In order to describe these large genetic reservoirs the pan-genome concept was introduced [1]. According to this concept, the species genome is composed of a core genome, containing genes present in all (or most) strains and a variable genome, containing genes present only in some strains.In some cases, this variation is concentrated in hypervariable sets of genes, known as genomic islands [2-4]. Genomic island genes are often involved in specific lifestyles [5,6], e.g. symbiosis or pathogenesis [7,8] and frequently have the hallmarks of horizontally transferred genetic material such as different GC content or codon usage [9,10]. However, very little is known about the dynamic processes that originate and maintain the large genomic variability found in closely related prokaryotic genomes.Metagenomics provides a new way to look at the dynamics and flexibili

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