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Open Access Highly Accessed Research article

Analysis of intra-genomic GC content homogeneity within prokaryotes

Jon Bohlin12*, Lars Snipen3, Simon P Hardy1, Anja B Kristoffersen24, Karin Lagesen456, Torunn Dønsvik4, Eystein Skjerve1 and David W Ussery5

Author affiliations

1 Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, Ullevålsveien 72, P.O. Box 8146 Dep, NO-0033 Oslo, Norway

2 National Veterinary Institute, Section of epidemiology, Ullevålsveien 68, Pb 750 Sentrum, N-0106 Oslo, Norway

3 Norwegian University of Life Sciences, Department of Chemistry, Biotechnology and Food Sciences, Ås, Norway

4 University of Oslo, Department of Informatics, Pb. 1080, 0316 Oslo, Norway

5 Center for Biological Sequence Analysis, Department of Systems Biology, Comparative Genomics Unit, Technical University of Denmark, DK-2800 Lyngby, Denmark

6 Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Rikshospitalet, NO-0027 Oslo, Norway

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Citation and License

BMC Genomics 2010, 11:464  doi:10.1186/1471-2164-11-464

Published: 6 August 2010

Abstract

Background

Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low GCVAR indicates intra-genomic GC homogeneity and high GCVAR heterogeneity.

Results

The regression analyses indicated that GCVAR was significantly associated with domain (i.e. archaea or bacteria), phylum, and oxygen requirement. GCVAR was significantly higher among anaerobes than both aerobic and facultative microbes. Although an association has previously been found between mean genomic GC content and oxygen requirement, our analysis suggests that no such association exits when phylogenetic bias is accounted for. A significant association between GCVAR and mean GC content was also found but appears to be non-linear and varies greatly among phyla.

Conclusions

Our findings show that GCVAR is linked with oxygen requirement, while mean genomic GC content is not. We therefore suggest that GCVAR should be used as a complement to mean GC content.