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

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 analysi...

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Bibliographic Details
Published in:Nature communications Vol. 9; no. 1; pp. 5114 - 8
Main Authors: Jain, Chirag, Rodriguez-R, Luis M., Phillippy, Adam M., Konstantinidis, Konstantinos T., Aluru, Srinivas
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 30.11.2018
Nature Publishing Group
Nature Portfolio
Subjects:
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631/326
Alignment
Biodiversity
Boundaries
Databases, Factual
Discontinuity
Gene mapping
Genetic diversity
Genetic Variation - genetics
Genome, Bacterial - genetics
Genomes
Humanities and Social Sciences
Mapping
Microbiology
multidisciplinary
Nucleotides
Phylogeny
Prokaryotic Cells - metabolism
Questions
Robustness
Science
Science (multidisciplinary)
Sequence Analysis, DNA
Species
ISSN:2041-1723, 2041-1723
Online Access:Get full text
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Summary: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 <83% inter-species ANI values. This discontinuity is manifested with or without the most frequently sequenced species, and is robust to historic additions in the genome databases. Average Nucleotide Identity (ANI) is a robust and useful measure to gauge genetic relatedness between two genomes. Here, the authors develop FastANI, a method to compute ANI using alignment-free approximate sequence mapping, and show 95% ANI is an accurate threshold for demarcating prokaryotic species by analyzing about 90,000 prokaryotic genomes.
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ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-018-07641-9