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

DOI DOI DOI HANDLE PDF ほか1件をすべて表示 一部だけ表示 被引用文献4件 参考文献68件
  • Wenyu Shi
    Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Qinglan Sun
    Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Guomei Fan
    Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Sugawara Hideaki
    National Institute of Genetics, Yata, Mishima 411-8540, Japan
  • Ohkuma Moriya
    Japan Collection of Microorganisms (JCM)/ Microbe Divion, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
  • Takashi Itoh
    Japan Collection of Microorganisms (JCM)/ Microbe Divion, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
  • Yuguang Zhou
    China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Man Cai
    China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Song-Gun Kim
    Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
  • Jung-Sook Lee
    Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
  • Ivo Sedlacek
    Czech Collection of Microorganisms, Masaryk University, Kamenice 5, building A25, 625 00 Brno, Czech Republic
  • David R Arahal
    Colección Española de Cultivos Tipo (CECT), and Departamento de Microbiología y Ecología, University of Valencia, 46100 Burjassot (Valencia), Spain
  • Teresa Lucena
    Colección Española de Cultivos Tipo (CECT), and Departamento de Microbiología y Ecología, University of Valencia, 46100 Burjassot (Valencia), Spain
  • Hiroko Kawasaki
    NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
  • Lyudmila Evtushenko
    All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow region 142290, Russia
  • Bevan S Weir
    Mycology & Bacteriology Systematics, Manaaki Whenua – Landcare Research, Auckland, New Zealand
  • Sarah Alexander
    National Collection of Type Cultures (NCTC), Public Health England (PHE), UK
  • Dlauchy Dénes
    National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, H-1118, Budapest, Somlói út 14-16, Hungary
  • Somboon Tanasupawat
    Faculty of Pharmaceutical Sciences, Chulalongkorn University (PCU), Bangkok 10330, Thailand
  • Lily Eurwilaichitr
    China-Thailand Joint Laboratory on Microbial Biotechnology, Beijing 100190, China
  • Supawadee Ingsriswang
    China-Thailand Joint Laboratory on Microbial Biotechnology, Beijing 100190, China
  • Bruno Gomez-Gil
    CIAD, A.C., Collection of Aquatic Important Microorganisms (CAIM). AP 711 Mazatlán, Sinaloa, Mexico
  • Manzour H Hazbón
    American Type Culture Collection(ATCC), 10801 University Boulevard, Manassas, VA 20110, USA
  • Marco A Riojas
    American Type Culture Collection(ATCC), 10801 University Boulevard, Manassas, VA 20110, USA
  • Chatrudee Suwannachart
    Biodiversity Research Centre, Thailand Institute of Scientific and Technological Research (TISTR), 35 M 3 Technopolis Khlong 5 Khlong Luang Pathum Thani 12120, Thailand
  • Su Yao
    China Center of Industrial Culture Collection (CICC), Beijing, China
  • Peter Vandamme
    BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
  • Fang Peng
    China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China
  • Zenghui Chen
    Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Dongmei Liu
    Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Xiuqiang Sun
    Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Xinjiao Zhang
    Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Yuanchun Zhou
    Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
  • Zhen Meng
    Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
  • Linhuan Wu
    Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
  • Juncai Ma
    Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China

書誌事項

公開日
2020-10-29
資源種別
journal article
権利情報
  • http://creativecommons.org/licenses/by/4.0/
DOI
  • 10.1093/nar/gkaa957
  • 10.60692/8fng2-4ec93
  • 10.60692/dwza5-eqx64
公開者
Oxford University Press (OUP)

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説明

<jats:title>Abstract</jats:title> <jats:p>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 &gt;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/.</jats:p>

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