Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

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

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DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recognition of novel species, but also allowed a relatively high degree of standardization compared to other areas of taxonomy. However, DDH is tedious and error-prone and first and foremost cannot be used to incrementally establish a comparative database. Recent studies have shown that in-silico methods for the comparison of genome sequences can be used to replace DDH. Considering the ongoing rapid technological progress of sequencing methods, genome-based prokaryote taxonomy is coming into reach. However, calculating distances between genomes is dependent on multiple choices for software and program settings. We here provide an overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented. General recommendations on determining HSPs using BLAST or other algorithms are also provided. As a reference implementation, we introduce the GGDC web server (http://ggdc.gbdp.org).

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/cf86f81718591aefb132398f7482a837814c8758

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Citations in the corpus

Genome sequence-based species delimitation with confidence intervals and improved distance functions (2013, methodology): “A further use of GBDP was recently evaluated, namely to infer digital equivalents for DDH values [8,16].”
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison (2010, methodology): “Because the range of investigated methods was broader than in previous studies, we were able to provide an accompanying standard operating procedure Standards in Genomic Sciences tion available as a web service for genome-based species delineation [29].”
VICTOR: genome-based phylogeny and classification of prokaryotic viruses (2017, methodology): “These techniques have previously been made available as an easy-to-use web service (Auch et al. 2010a; Auch et al. 2010b).”