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Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy

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  • Yuval Bussi
  • Ruti Kapon
  • Ziv Reich

Abstract

Information theoretic approaches are ubiquitous and effective in a wide variety of bioinformatics applications. In comparative genomics, alignment-free methods, based on short DNA words, or k-mers, are particularly powerful. We evaluated the utility of varying k-mer lengths for genome comparisons by analyzing their sequence space coverage of 5805 genomes in the KEGG GENOME database. In subsequent analyses on four k-mer lengths spanning the relevant range (11, 21, 31, 41), hierarchical clustering of 1634 genus-level representative genomes using pairwise 21- and 31-mer Jaccard similarities best recapitulated a phylogenetic/taxonomic tree of life with clear boundaries for superkingdom domains and high subtree similarity for named taxons at lower levels (family through phylum). By analyzing ~14.2M prokaryotic genome comparisons by their lowest-common-ancestor taxon levels, we detected many potential misclassification errors in a curated database, further demonstrating the need for wide-scale adoption of quantitative taxonomic classifications based on whole-genome similarity.

Suggested Citation

  • Yuval Bussi & Ruti Kapon & Ziv Reich, 2021. "Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy," PLOS ONE, Public Library of Science, vol. 16(10), pages 1-27, October.
    • Handle: RePEc:plo:pone00:0258693
    DOI: 10.1371/journal.pone.0258693
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    References listed on IDEAS

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