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gcType: a high-quality type strain genome database for microbial phylogenetic and functional research

W. Shi, Q. Sun, G. Fan, S. Hideaki, O. Moriya, T. Itoh, Y. Zhou, M. Cai, SG. Kim, JS. Lee, I. Sedlacek, DR. Arahal, T. Lucena, H. Kawasaki, L. Evtushenko, BS. Weir, S. Alexander, D. Dénes, S. Tanasupawat, L. Eurwilaichitr, S. Ingsriswang, B....

. 2021 ; 49 (D1) : D694-D705. [pub] 20210108

Jazyk angličtina Země Velká Británie

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc21011620

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/.

All Russian Collection of Microorganisms G K Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS Pushchino Moscow region 142290 Russia

American Type Culture Collection 10801 University Boulevard Manassas VA 20110 USA

BCCM LMG Bacteria Collection Laboratory of Microbiology Faculty of Sciences Ghent University K L Ledeganckstraat 35 9000 Ghent Belgium

Biodiversity Research Centre Thailand Institute of Scientific and Technological Research 35 M 3 Technopolis Khlong 5 Khlong Luang Pathum Thani 12120 Thailand

China Center for Type Culture Collection College of Life Sciences Wuhan University Wuhan 430072 China

China Center of Industrial Culture Collection Beijing China

China General Microbiological Culture Collection Center Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China

China Thailand Joint Laboratory on Microbial Biotechnology Beijing 100190 China

CIAD A C Collection of Aquatic Important Microorganisms AP 711 Mazatlán Sinaloa Mexico

Colección Española de Cultivos Tipo Spain

Computer Network Information Center Chinese Academy of Sciences Beijing 100190 China

Czech Collection of Microorganisms Masaryk University Kamenice 5 building A25 625 00 Brno Czech Republic

Faculty of Pharmaceutical Sciences Chulalongkorn University Bangkok 10330 Thailand

Japan Collection of Microorganisms Microbe Divion RIKEN BioResource Center Koyadai 3 1 1 Tsukuba Ibaraki 305 0074 Japan

Korean Collection for Type Cultures 181 Ipsin gil Jeongeup si Jeollabuk do 56212 Republic of Korea

Microbial Resource and Big Data Center Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China

Mycology and Bacteriology Systematics Manaaki Whenua Landcare Research Auckland New Zealand

National Collection of Agricultural and Industrial Microorganisms Faculty of Food Science Szent István University H 1118 Budapest Somlói út 14 16 Hungary

National Collection of Type Cultures UK

National Institute of Genetics Yata Mishima 411 8540 Japan

NITE Biological Resource Center National Institute of Technology and Evaluation 2 5 8 Kazusakamatari Kisarazu Chiba 292 0818 Japan

State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China

Thailand Bioresource Research Center Thailand

World Data Center for Microorganisms Beijing 100101 China

Citace poskytuje Crossref.org

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