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International Journal of Systematic and Evolutionary Microbiology

Volume 68, Issue 7

Research Article

Open Access

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

• Stacy Ciufo1, Sivakumar Kannan1, Shobha Sharma1, Azat Badretdin1, Karen Clark1, Seán Turner1, Slava Brover1, Conrad L. Schoch1, Avi Kimchi1 and Michael DiCuccio1
• View Affiliations Hide Affiliations 1 National Center of Biotechnology Information, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA *Correspondence: Stacy Ciufo, [email protected]
• Published: 01 July 2018 https://doi.org/10.1099/ijsem.0.002809

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Abstract

Average nucleotide identity analysis is a useful tool to verify taxonomic identities in prokaryotic genomes, for both complete and draft assemblies. Using optimum threshold ranges appropriate for different prokaryotic taxa, we have reviewed all prokaryotic genome assemblies in GenBank with regard to their taxonomic identity. We present the methods used to make such comparisons, the current status of GenBank verifications, and recent developments in confirming species assignments in new genome submissions.

• Received: 07/12/2017
• Accepted: 26/04/2018
• Published Online: 01/07/2018

Keyword(s): GenBank , RefSeq , taxonomy and type strains © 2018 IUMS

• This is an open access article under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.

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/content/journal/ijsem/10.1099/ijsem.0.002809 Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI Int J Syst Evol Microbiol 68, 2386 (2018); https://doi.org/10.1099/ijsem.0.002809 /content/journal/ijsem/10.1099/ijsem.0.002809 /content/journal/ijsem/10.1099/ijsem.0.002809

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