Analysis of intra-genomic GC content homogeneity within prokaryotes.
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.
Bohlin
Jon
J
Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, Ullevålsveien 72, P,O, Box 8146 Dep, NO-0033 Oslo, Norway. jon.bohlin@veths.no
Snipen
Lars
L
Hardy
Simon P
SP
Kristoffersen
Anja B
AB
Lagesen
Karin
K
Dønsvik
Torunn
T
Skjerve
Eystein
E
Ussery
David W
DW
D000332:Aerobiosis; D000693:Anaerobiosis; D001482:Base Composition; D016678:Genome; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000737:chemistry* / Q000378:metabolism; D012044:Regression Analysis