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

Author

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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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    1. Chirag Jain & Luis M. Rodriguez-R & Adam M. Phillippy & Konstantinos T. Konstantinidis & Srinivas Aluru, 2018. "High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    2. Fionn Murtagh & Pierre Legendre, 2014. "Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?," Journal of Classification, Springer;The Classification Society, vol. 31(3), pages 274-295, October.
    3. Alexandra M Schnoes & Shoshana D Brown & Igor Dodevski & Patricia C Babbitt, 2009. "Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies," PLOS Computational Biology, Public Library of Science, vol. 5(12), pages 1-13, December.
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