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

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.

[1]  Natalia N. Ivanova,et al.  1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life , 2017, Nature Biotechnology.

[2]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[3]  Natalia N. Ivanova,et al.  Microbial species delineation using whole genome sequences , 2015, Nucleic acids research.

[4]  Piotr Indyk,et al.  Approximate nearest neighbors: towards removing the curse of dimensionality , 1998, STOC '98.

[5]  Scott Federhen,et al.  The NCBI Taxonomy database , 2011, Nucleic Acids Res..

[6]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[7]  J. Chun,et al.  Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. , 2014, International Journal of Systematic and Evolutionary Microbiology.

[8]  Heike Sichtig,et al.  Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015) , 2016, Standards in Genomic Sciences.

[9]  Lawrence G. Wayne,et al.  International Committee on Systematic Bacteriology announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. , 1988, The Journal of applied bacteriology.

[10]  K. Konstantinidis,et al.  Genomic insights that advance the species definition for prokaryotes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Scott Federhen,et al.  Type material in the NCBI Taxonomy Database , 2014, Nucleic Acids Res..

[12]  J. Chun,et al.  A large-scale evaluation of algorithms to calculate average nucleotide identity , 2017, Antonie van Leeuwenhoek.

[13]  George M Garrity,et al.  International Code of Nomenclature of Prokaryotes. , 2015, International journal of systematic and evolutionary microbiology.

[14]  P. Bork,et al.  Accurate and universal delineation of prokaryotic species , 2013, Nature Methods.

[15]  Tatiana A. Tatusova,et al.  Update on RefSeq microbial genomes resources , 2014, Nucleic Acids Res..

[16]  R. Rosselló-Móra,et al.  Shifting the genomic gold standard for the prokaryotic species definition , 2009, Proceedings of the National Academy of Sciences.

[17]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2010, Nucleic Acids Res..

[18]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..