Abstract
In the original proposal of Wayne et al. (Int J Syst Bacteriol 37:463–464, 1987), two measures of genetic relatedness were proposed to set the boundary for prokaryotic species. The first was the change in the melting temperature (ΔTm) of heteroduplex DNA and the second was the extent of DNA–DNA hybridization (DDH). While this approach was justified given the experimental error inherent in these methods, genomic sequencing has the potential to measure both parameters with great precision. The average nucleotide identity (ANIb), a surrogate for the ΔTm, and the calculated DDH (cDDH) were determined from the complete genomes of representatives of 17 genera of prokaryotes. When the ANIb was >75 %, the ratio (100-cDDH)/(100-ANIb) was 3.69 ± 0.93 (± SD) and varied from about 2.35 to 4.59 between genera. The differences among genera was highly significant (p < 0.001) but not correlated with specific phylogenetic or physiological groups. Moreover, the ANIm was a poor measure of ANIb when ANIb was <75 %. Because the ANIb and cDDH provide different measures of relatedness, it is no longer appropiate to consider both when delineating species. For these reasons, measures of relatedness based upon sequence identity should be used for delineating species in the future.
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Acknowledgments
The authors are grateful to Dale Boyer of the Department of Microbiology of the University of Georgia for assistance with installing of software for these calculations. This work was supported in part by the National Natural Science Foundation of China (No. 31170537, 31270612) and Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), the Office of the Vice-President for Research at the University of Georgia, and a NSF Dimensions of Biodiversity grant.
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Li, X., Huang, Y. & Whitman, W.B. The relationship of the whole genome sequence identity to DNA hybridization varies between genera of prokaryotes. Antonie van Leeuwenhoek 107, 241–249 (2015). https://doi.org/10.1007/s10482-014-0322-1
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DOI: https://doi.org/10.1007/s10482-014-0322-1