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Trends between gene content and genome size in prokaryotic species

Trends between gene content and genome size in prokaryotic species

Abstracts of the General Meeting of the American Society for Microbiology 103: R-046

To determine whether there are universal trends between the relative number of genes attributable to specific cellular functions and genome size, we functionally characterized the fully sequenced prokaryotic genomes (81 genomes as of July 2002) using the COGs database. COGs provides convenient means of annotation by grouping all proteins in eighteen functional categories. All possible ORFs from the 81 genomes were assigned to a functional category according to the category where their best COG homolog has been classified. Our results showed that the portion of the genome devoted to translation and biogenesis, DNA replication and repair, nucleotide transport and metabolism, was negatively correlated with genome size, whereas the portion devoted to transcription, signal transduction, inorganic ion transport, amino acid and carbohydrate transport and metabolism, secondary metabolite biosynthesis and unknown function (or conserved hypothetical) was positively correlated. The remaining categories showed no correlation with genome size. These results are supported by our independent analysis of the publicly available data from TIGR's CMR and KEGG's Orthology databases. It is thus conclusive that large genomes preferentially accumulate metabolic, transport and regulatory genes as opposed to informational ones. These results correlate with the metabolic versatility and boarder ecological success shown by species with larger genomes and predict that such species are more successful in diverse resource habitats. However genomic data is currently heavily biased towards small genome clinical strains make it difficult to evaluate the origins of the larger genomes. Archaea, compared to Bacteria of the same genome size, had proportionally more genes in energy production and poorly characterized categories and fewer in cell envelope biogenesis and cell motility and secretion systems. Lastly, our analysis of the 23 environmental strains partially sequenced by JGI showed that JGI's genomes poorly matched COG database compared to the fully sequenced ones, indicating that they posses more of the uncharacterized genes in nature.

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Accession: 035985122

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