Estimation of prokaryote genomic DNA G+C content by sequencing universally conserved genes.
Determination of the DNA G+C content of prokaryotic genomes using traditional methods is time-consuming and results may vary from laboratory to laboratory, depending on the technique used. We explored the possibility of extrapolating the genomic DNA G+C content of prokaryotes from gene sequences. For this, 127 universally conserved genes were studied from 50 prokaryotic genomes in the Clusters of Orthologous Groups database. Of these, 57 genes were present as a single copy in the genomes of 157 different prokaryote species available in GenBank. There was a strong correlation [coefficient of determination (r2) >95 %] between the DNA G+C contents of 20 genes and their corresponding genomes. For each of the 157 prokaryotic genomes studied, the DNA G+C content of the 20 genes was used to determine a 'calculated' genome DNA G+C content (CGC) and this value was compared with the 'real' genome DNA G+C content (RGC). In order to select the most suitable gene for the determination of CGC values, we compared the r2 and median mol% difference between CGC and RGC as well as the sensitivity of each gene to provide CGC values for prokaryotic genomes that differ by less than 5 mol% from their RGC. The highly conserved ftsY gene (median size 1144 nucleotides), a vertically inherited member of the GTPase superfamily, showed the highest r2 value of 0.98, the smallest median mol% difference between CGC and RGC of 1.06 and a sensitivity of 100 %. Using ftsY DNA G+C content values, the CGC values of 100 genomes not included in the calculation of r2 differed by less than 5 mol% from their RGC values. These data suggest that the genomic DNA G+C content of prokaryotes may be estimated easily and reliably from the ftsY gene sequence.
Fournier
Pierre-Edouard
PE
Information Génomique et Structurale, CNRS UPR2589, Case 934, 163 Avenue de Luminy, 13288 Marseille cedex 09, France.
Suhre
Karsten
K
Information Génomique et Structurale, CNRS UPR2589, Case 934, 163 Avenue de Luminy, 13288 Marseille cedex 09, France.
Fournous
Ghislain
G
Unité des rickettsies, IFR 48, CNRS UMR 6020, Faculté de Médecine, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France.
Raoult
Didier
D
Unité des rickettsies, IFR 48, CNRS UMR 6020, Faculté de Médecine, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France.
D001419:Bacteria / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D001482:Base Composition; D019295:Computational Biology; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D008967:Molecular Biology / Q000379:methods*; D018160:Receptors, Cytoplasmic and Nuclear / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D013223:Statistics as Topic
D001426:Bacterial Proteins; D004269:DNA, Bacterial; C087406:FtsY protein, Bacteria; D018160:Receptors, Cytoplasmic and Nuclear