The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species

Linhuan Wu^{1

2

3}, Kevin McCluskey^{4

5}, Philippe Desmeth^{4

6}, Shuangjiang Liu^{2

4}, Sugawara Hideaki⁷, Ye Yin⁸, Ohkuma Moriya⁹, Takashi Itoh⁹, Cha Young Kim¹⁰, Jung-Sook Lee¹⁰, Yuguang Zhou¹¹, Hiroko Kawasaki¹², Manzour Hernando Hazbón¹³, Vincent Robert¹⁴, Teun Boekhout^{14

15

16}, Nelson Lima¹⁷, Lyudmila Evtushenko¹⁸, Kyria Boundy-Mills^{4

19}, Boyke Bunk²⁰, Edward R B Moore²¹, Lily Eurwilaichitr^{4

22}, Supawadee Ingsriswang²², Heena Shah²³, Su Yao²⁴, Tao Jin⁸, Jinqun Huang⁸, Wenyu Shi¹, Qinglan Sun¹, Guomei Fan¹, Wei Li¹, Xian Li¹, Ipek Kurtböke^{4

25}, Juncai Ma^{1

2

3

4}

Affiliations

¹ Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
² State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
³ WFCC-MIRCEN World Data Center for Microorganisms, Beijing 100101, China.
⁴ World Federation of Culture Collections (WFCC).
⁵ Fungal Genetics Stock Center, Kansas State University, Manhattan, KS 66506, USA.
⁶ Belgian Coordinated Collections of Micro-organisms Program, Belgian Science Policy Office, Brussels 231 1050, Belgium.
⁷ National Institute of Genetics, Yata, Mishima 411-8540, Japan.
⁸ BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
⁹ Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan.
¹⁰ Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea.
¹¹ China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing10010, China.
¹² NITE Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan.
¹³ American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110, USA.
¹⁴ Westerdijk Fungal Biodiversity Institue, Utrecht 3534CT, Netherlands.
¹⁵ Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Spui 21 1012 WX Amsterdam, Netherlands.
¹⁶ Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Shanghai 200003, China.
¹⁷ Micoteca da Universidade do Minho, Biological Engineering Centre, 4710-057 Braga, Portugal.
¹⁸ All-Russian Collection of Microorganisms, GK Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region 142290, Russia.
¹⁹ Phaff Yeast Culture Collection, Food Science and Technology Department, University of California Davis, 1 Shields Avenue, Davis, CA 95616-8598, USA.
²⁰ Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, D-38124 Braunschweig, Germany.
²¹ Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, SE-41346 Gothenburg, Sweden.
²² Bioresources Technology Unit, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, Bangkok National Science and Technology Development Agency, 113, Thailand.
²³ National Collection of Type Cultures, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, UK.
²⁴ China Center of Industrial Culture Collection, Beijing 100015, China.
²⁵ Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4558, Australia.

PMID: 29718202
PMCID: PMC5941136
DOI: 10.1093/gigascience/giy026

The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species

Linhuan Wu et al. Gigascience. 2018.

. 2018 May 1;7(5):giy026.

doi: 10.1093/gigascience/giy026.

Authors

Affiliations

¹ Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
² State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
³ WFCC-MIRCEN World Data Center for Microorganisms, Beijing 100101, China.
⁴ World Federation of Culture Collections (WFCC).
⁵ Fungal Genetics Stock Center, Kansas State University, Manhattan, KS 66506, USA.
⁶ Belgian Coordinated Collections of Micro-organisms Program, Belgian Science Policy Office, Brussels 231 1050, Belgium.
⁷ National Institute of Genetics, Yata, Mishima 411-8540, Japan.
⁸ BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
⁹ Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan.
¹⁰ Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea.
¹¹ China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing10010, China.
¹² NITE Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan.
¹³ American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110, USA.
¹⁴ Westerdijk Fungal Biodiversity Institue, Utrecht 3534CT, Netherlands.
¹⁵ Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Spui 21 1012 WX Amsterdam, Netherlands.
¹⁶ Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Shanghai 200003, China.
¹⁷ Micoteca da Universidade do Minho, Biological Engineering Centre, 4710-057 Braga, Portugal.
¹⁸ All-Russian Collection of Microorganisms, GK Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow Region 142290, Russia.
¹⁹ Phaff Yeast Culture Collection, Food Science and Technology Department, University of California Davis, 1 Shields Avenue, Davis, CA 95616-8598, USA.
²⁰ Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, D-38124 Braunschweig, Germany.
²¹ Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, SE-41346 Gothenburg, Sweden.
²² Bioresources Technology Unit, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, Bangkok National Science and Technology Development Agency, 113, Thailand.
²³ National Collection of Type Cultures, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, UK.
²⁴ China Center of Industrial Culture Collection, Beijing 100015, China.
²⁵ Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4558, Australia.

PMID: 29718202
PMCID: PMC5941136
DOI: 10.1093/gigascience/giy026

Abstract

Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microorganisms. Hence, the GCM aims to promote research by deep-mining genomic data.

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References

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The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species

Affiliations

The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species

Authors

Affiliations

Abstract

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical