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Large-scale evaluation of experimentally determined DNA G plus C contents with whole genome sequences of prokaryotes

Cited 11 time in Web of Science Cited 11 time in Scopus
Authors
Kim, Mincheol; Park, Sang-Cheol; Baek, Inwoo; Chun, Jongsik
Issue Date
2015-03
Citation
Systematic and Applied Microbiology, Vol.38 No.2, pp.79-83
Keywords
DNA G plus C contentWhole genome sequencesProkaryote taxonomyAverage nucleotide identity
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 16x or higher sequencing depth of coverage. (C) 2014 Elsevier GmbH. All rights reserved.
ISSN
0723-2020
URI
https://hdl.handle.net/10371/165747
DOI
https://doi.org/10.1016/j.syapm.2014.11.008
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College of Natural Sciences (자연과학대학)Dept. of Biological Sciences (생명과학부)Journal Papers (저널논문_생명과학부)
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