title: Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes.
abstract: Historically, DNA G+C content has played a critical role in the description of bacterial and archaeal species. Despite its importance in prokaryote taxonomy, its accuracy has been questioned due to methodological heterogeneity and measurement errors of conventional methods. Here we investigated the extent of accuracy of experimentally determined DNA G+C contents by comparing the reference values calculated from whole genome sequences. The large-scale comparison revealed that G+C contents determined by high-performance liquid chromatography and buoyant density centrifugation methods were more similar to the genome-derived reference values than those generated by thermal denaturation method. However, there was a substantial degree of discrepancy in DNA G+C contents between values obtained by conventional methods and genome-derived reference values. The majority of the differences between them fell out of the acceptable range (i.e. 1 mol% G+C content difference) for species delimitation of prokaryotes. In contrast, when average nucleotide identity (ANI) was correlated to G+C difference among genomes, most G+C difference was confined to less than 1% within species. Therefore, erroneous conventional methods are not meaningful in the description of bacterial and archaeal species. For taxonomic purposes, DNA G+C content should be determined by calculating directly from high-quality genome sequences with at least 16× or higher sequencing depth of coverage.
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea.
authors.forename: Mincheol
authors.initials: M
authors.lastname: Kim
authors.affiliation: Interdisciplinary Program in Bioinformatics and Bioinformatics Institute, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Sang-Cheol
authors.initials: SC
authors.lastname: Park
authors.affiliation: School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Inwoo
authors.initials: I
authors.lastname: Baek
authors.affiliation: School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea; Interdisciplinary Program in Bioinformatics and Bioinformatics Institute, Seoul National University, Seoul 151-742, Republic of Korea. Electronic address: jchun@snu.ac.kr.
authors.forename: Jongsik
authors.initials: J
authors.lastname: Chun
mesh_terms: D001105:Archaea / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D001419:Bacteria / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D001482:Base Composition; D002623:Chemistry Techniques, Analytical; D019641:DNA, Archaeal / Q000737:chemistry* / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D008828:Microbiological Techniques; D008967:Molecular Biology / Q000379:methods
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial
keywords: Average nucleotide identity; DNA G+C content; Prokaryote taxonomy; Whole genome sequences