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gcType: A high-quality type strain genome database for microbial phylogenetic and functional research
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Document Title
gcType: A high-quality type strain genome database for microbial phylogenetic and functional research
Author
Shi W.,Sun Q.,Fan G.,Hideaki S.,Moriya O.,Itoh T.,Zhou Y.,Cai M.,Kim S.-G.,Lee J.-S.,Sedlacek I.,Arahal D.R.,Lucena T.,Kawasaki H.,Evtushenko L.,Weir B.S.,Alexander S.,Dénes D.,Tanasupawat S.,Eurwilaichitr L.,Ingsriswang S.,Gomez-Gil B.,Hazbón M.H.,Riojas M.A.,Suwannachart C.,Yao S.,Vandamme P.,Peng F.,Chen Z.,Liu D.,Sun X.,Zhang X.,Zhou Y.,Meng Z.,Wu L.,Ma J.
Name from Authors Collection
Affiliations
Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; World Data Center for Microorganisms, Beijing, 100101, China; China-Thailand Joint Laboratory on Microbial Biotechnology, Beijing, 100190, China; National Institute of Genetics, Yata, Mishima, 411-8540, Japan; Japan Collection of Microorganisms (JCM)/ Microbe Divion, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki, 305-0074, Japan; China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, South Korea; Czech Collection of Microorganisms, Masaryk University, Kamenice 5, building A25, Brno, 625 00, Czech Republic; Colección Española de Cultivos Tipo (CECT), Departamento de Microbiología y Ecología, University of Valencia, Burjassot (Valencia), 46100, Spain; NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan; All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow region, 142290, Russian Federation; Mycology and Bacteriology Systematics, Manaaki Whenua - Landcare Research, Auckland, New Zealand; National Collection of Type Cultures (NCTC), Public Health England (PHE), United Kingdom; National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Somlói út 14-16, Budapest, H-1118, Hungary; Faculty of Pharmaceutical Sciences, Chulalongkorn University (PCU), Bangkok, 10330, Thailand; Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand; CIAD, A.C., Collection of Aquatic Important Microorganisms (CAIM), AP 711 Mazatlán, Sinaloa, Mexico; American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, United States; Biodiversity Research Centre, Thailand Institute of Scientific and Technological Research (TISTR), 35 M 3 Technopolis Khlong 5, Khlong Luang Pathum Thani, 12120, Thailand; China Center of Industrial Culture Collection (CICC), Beijing, China; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, Ghent, 9000, Belgium; China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China; Computer Network Information Center, Chinese Academy of Sciences, Beijing, 100190, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
Type
Article
Source Title
Nucleic Acids Research
ISSN
03051048
Year
2021
Volume
49
Issue
D1
Page
D694-D705
Open Access
All Open Access, Gold, Green
Publisher
Oxford University Press
DOI
10.1093/nar/gkaa957
Abstract
Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
License
CC BY-NC
Rights
Author
Publication Source
Scopus