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

By S. Ciufo, S. Kannan, Shobha Sharma, Azat Badretdin, Karen Clark, S. Turner, Slava Brover, C. Schoch, Avi Kimchi, Michael DiCuccio. International Journal of Systematic and Evolutionary Microbiology, 2018

425 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9500c25cc648dbb1ed3b501a840791fc7431c7f4

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In Molecular Biology

Citations in the corpus

NCBI Taxonomy: a comprehensive update on curation, resources and tools (2020, methodology): “As part of the NCBI prokaryotic genome submission process, GenBank now performs an average nucleotide identity analysis to identify and correct misiden-tified genomes during submissions (51).”
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation (2020, methodology): “…only rarely, RefSeq regularly reannotates genomes with PGAP, the Prokaryotic Genome Annotation Pipeline (1,2), to reflect newly characterized prokaryotic metabolic and regulatory systems published in the literature and in specialized resources (3,4) and taxonomic re-assignment of genomes (5).”