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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Author

Listed:
  • Chirag Jain

    (Georgia Institute of Technology
    National Institutes of Health)

  • Luis M. Rodriguez-R

    (Georgia Institute of Technology
    Georgia Institute of Technology)

  • Adam M. Phillippy

    (National Institutes of Health)

  • Konstantinos T. Konstantinidis

    (Georgia Institute of Technology
    Georgia Institute of Technology)

  • Srinivas Aluru

    (Georgia Institute of Technology
    Georgia Institute of Technology)

Abstract

A fundamental question in microbiology is whether there is continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome similarity metrics such as Average Nucleotide Identity (ANI) help address this question by facilitating high resolution taxonomic analysis of thousands of genomes from diverse phylogenetic lineages. To scale to available genomes and beyond, we present FastANI, a new method to estimate ANI using alignment-free approximate sequence mapping. FastANI is accurate for both finished and draft genomes, and is up to three orders of magnitude faster compared to alignment-based approaches. We leverage FastANI to compute pairwise ANI values among all prokaryotic genomes available in the NCBI database. Our results reveal clear genetic discontinuity, with 99.8% of the total 8 billion genome pairs analyzed conforming to >95% intra-species and

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-07641-9
    DOI: 10.1038/s41467-018-07641-9
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