Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

By Alexander F. Auch, M. von Jan, Hans-Peter Klenk, Markus Göker. Standards in Genomic Sciences, 2010

1,622 citations recorded by the source corpus.

The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.

Subfields: Ecology, Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9d6d5c466c46c1045ee83ca700dc14c34692e8b1

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Citations in the corpus

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs (2010, methodology): “Algorithms to efficiently determine high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) are valuable tools for inferring intergenomic distances for species delimitation (see [1] and references therein).”
Genome sequence-based species delimitation with confidence intervals and improved distance functions (2013, methodology): “To detect significant deviations, if any, between the new and the previous GBDP implementation, the data subset “DS2” was created, containing only the previously available data points [8].”
Pseudomonas aeruginosa population structure revisited under environmental focus (2010, methodology): “In the current genome era propositions of new, several genome sequence based algorithms for the species affiliation emerge, which are meant to replace the laboratory work of DNA-DNA hybridization (Auch et al., 2010; Richter & Rossello-Mora, 2009).”
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes (2021, positive): “The distances are used for phylogenetic inference and also form the basis for the dDDH method, one of the most widely used overall genome relatedness indices (OGRI) for in silico species delineation (18,19).”