Collection and curation of prokaryotic genome assemblies from type strains at NCBI.
ANI
GenBank
genome
taxonomy
type material
type strain
Journal
International journal of systematic and evolutionary microbiology
ISSN: 1466-5034
Titre abrégé: Int J Syst Evol Microbiol
Pays: England
ID NLM: 100899600
Informations de publication
Date de publication:
Feb 2023
Feb 2023
Historique:
entrez:
7
2
2023
pubmed:
8
2
2023
medline:
9
2
2023
Statut:
ppublish
Résumé
The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verification or reclassification. The National Center for Biotechnology Information (NCBI) collects and curates information on prokaryotic type strains and genomes from type strains. The average nucleotide identity (ANI)-based quality control processes introduced at NCBI to verify the genomes from type strains and improve related sequence records are detailed here. Using the curated genomes from type strains as reference, the taxonomy of over 1.1 million GenBank genomes were verified and the taxonomy of over 7000 new submissions before acceptance to GenBank and over 1800 existing genomes in GenBank were reclassified.
Identifiants
pubmed: 36748495
doi: 10.1099/ijsem.0.005707
pmc: PMC10228379
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
DNA, Bacterial
0
Fatty Acids
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Références
PLoS One. 2013 Dec 30;8(12):e83357
pubmed: 24386187
Database (Oxford). 2020 Jan 1;2020:
pubmed: 32761142
Gut Pathog. 2021 Jan 12;13(1):3
pubmed: 33436056
Nucleic Acids Res. 2018 Jan 4;46(D1):D48-D51
pubmed: 29190397
Int J Syst Evol Microbiol. 2018 Jul;68(7):2125-2129
pubmed: 29873629
Int J Syst Evol Microbiol. 2020 Jul;70(7):4416-4417
pubmed: 32628106
Nucleic Acids Res. 2015 Jan;43(Database issue):D1086-98
pubmed: 25398905
Int J Syst Evol Microbiol. 2022 Sep;72(9):
pubmed: 36125864
Nat Biotechnol. 2020 Sep;38(9):1079-1086
pubmed: 32341564
Microbiol Resour Announc. 2019 May 30;8(22):
pubmed: 31147430
Int J Syst Evol Microbiol. 2016 Jun;66(6):2438-2443
pubmed: 27030978
Int J Syst Evol Microbiol. 2020 Nov;70(11):5607-5612
pubmed: 32701423
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Front Microbiol. 2021 Mar 25;12:614957
pubmed: 33841347
Trends Microbiol. 2021 May;29(5):394-404
pubmed: 33546975
Nucleic Acids Res. 2021 Jan 8;49(D1):D1020-D1028
pubmed: 33270901
Int J Syst Evol Microbiol. 2021 Nov;71(11):
pubmed: 34846285
Nat Microbiol. 2022 Oct;7(10):1702-1708
pubmed: 36123442
ISME J. 2021 Jul;15(7):1879-1892
pubmed: 33824426
New Microbes New Infect. 2021 Aug 13;43:100931
pubmed: 34484799
Int J Syst Evol Microbiol. 2020 Jul;70(7):3956-4042
pubmed: 32603289
Int J Syst Evol Microbiol. 2018 Jul;68(7):2386-2392
pubmed: 29792589
Res Microbiol. 2015 May;166(4):303-17
pubmed: 25445012
Int J Syst Evol Microbiol. 2021 Sep;71(9):
pubmed: 34516368
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2567-72
pubmed: 15701695