Bohlin et al. BMC Genomics 2010, 11:464 http://www.biomedcentral.com/1471-2164/11/464 R E S E A R C H A R T I C L E Open Access Analysis of intra-genomic GC content homogeneity within prokaryotes Jon Bohlin1,2*, Lars Snipen3, Simon P Hardy1, Anja B Kristoffersen2,4, Karin Lagesen4,5,6, Torunn Dønsvik4, Eystein Skjerve1, David W Ussery5 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. Background The knowledge of the chemical basis for nucleic acids goes back more than a hundred years, to the work of Miescher [1]. By the early 1950’s, it was known that the relative frequency of the four DNA bases ("base compo- sition”) was different for different organisms [2], and in general the number of A’s was equal to the number of T’s, and the number of G’s was the same as the number of C’s; this is known as ‘Chargaff’s first parity rule’ [3]. Further, for nearly all genomes studied, the parity rule appears to extend to each strand of the chromosome, when averaged over long distances [4], although in bac- terial chromosomes, there is a clear bias of G’s towards the replication leading strand, and for some genomes (many Firmicutes, for example) the A’s are also biased * Correspondence: jon.bohlin@veths.no 1Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, Ullevålsveien 72, P.O. Box 8146 Dep, NO-0033 Oslo, Norway Full list of author information is available at the end of the article towards the leading strand [5]. For a circular chromo- some with the replication origin and terminus on exactly opposite sides, this bias of G’s towards the repli- cation leading strand will average out to near zero, when one only looks at the DNA sequence in the Gen- Bank file, and the sequence will appear to conform to Chargaff’s second rule. From the Genbank database at NCBI http://www.ncbi. nlm.nih.gov/genomes/lproks.cgi it can be seen that GC content in prokaryotes ranges from 16.6% in Carsonella ruddii strain Pv to 74.9% in Anaeromyxobacter dehalo- genans Strain 2CP-C. Within a given genome, the GC content along the chromosome can vary, although since most bacterial genomes have a high coding density, usually the variation is less than that found in eukar- yotes [6]. The average genomic GC content is an impor- tant property in microbial genomes and has been associated with properties such as genome size [7], oxy- gen, and nitrogen exposure [8,9] and specific habitats [10-13]. For instance, intracellular bacteria have, on © 2010 Bohlin et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.