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


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Article Info

DATE

2010-01-28

AUTHORS

Alexander F. Auch, Mathias von Jan, Hans-Peter Klenk, Markus Göker

ABSTRACT

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. More... »

PAGES

117-134

References to SciGraph publications

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  • 2010-02-28. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T) in STANDARDS IN GENOMIC SCIENCES
  • 1975-12. Improvements of the membrane filter method for DNA:rRNA hybridization in ANTONIE VAN LEEUWENHOEK
  • 2009-07-20. Complete genome sequence of Desulfomicrobium baculatum type strain (XT) in STANDARDS IN GENOMIC SCIENCES
  • 2006. DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation in MOLECULAR IDENTIFICATION, SYSTEMATICS, AND POPULATION STRUCTURE OF PROKARYOTES
  • 1986-12. Hybridization homology: A new parameter for the analysis of phylogenetic relations, demonstrated with the urkingdom of the archaebacteria in JOURNAL OF MOLECULAR EVOLUTION
  • 2004-01. Versatile and open software for comparing large genomes in GENOME BIOLOGY
  • 2009-12. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea in NATURE
  • 2009-03-16. Bacterial Genome Sequencing in MOLECULAR EPIDEMIOLOGY OF MICROORGANISMS
  • 2001-12. Genome trees constructed using five different approaches suggest new major bacterial clades in BMC EVOLUTIONARY BIOLOGY
  • 2004-03-01. Pyrosequencing: A Tool for DNA Sequencing Analysis in BACTERIAL ARTIFICIAL CHROMOSOMES
  • 2010-01-28. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs in STANDARDS IN GENOMIC SCIENCES
  • 2008-12. General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability in BMC EVOLUTIONARY BIOLOGY
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    http://scigraph.springernature.com/pub.10.4056/sigs.531120

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    44 schema:description 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.
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