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

J 2021

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

SHI, Wenyu, Qinglan SUN, Guomei FAN, Sugawara HIDEAKI, Moriya OHKUMA et. al.

Základní údaje

Originální název

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

Autoři

SHI, Wenyu, Qinglan SUN, Guomei FAN, Sugawara HIDEAKI, Moriya OHKUMA, Takashi ITOH, Yuguang ZHOU, Man CAI, Song-Gun KIM, Jung-Sook LEE, Ivo SEDLÁČEK (203 Česká republika, domácí), David R. ARAHAL, Teresa LUCENA, Hiroko KAWASAKI, Lyudmila EVTUSHENKO, Bevan S. WEIR, Sarah ALEXANDER, Dlauchy DÉNES, Somboon TANASUPAWAT, Lily EURWILAICHITR, Supawadee INGSRISWANG, Bruno GOMEZ-GIL, Manzour H. HAZBÓN, Marco A. RIOJAS, Chatrudee SUWANNACHART, Su YAO, Peter VANDAMME, Fang PENG, Zenghui CHEN, Dongmei LIU, Xiuqiang SUN, Xinjiao ZHANG, Yuanchun ZHOU, Zhen MENG, Linhuan WU a Juncai MA

Vydání

Nucleic Acids Research, Oxford, Oxford University Press, 2021, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10606 Microbiology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 19.160

Kód RIV

RIV/00216224:14310/21:00120904

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1093/nar/gkaa957

UT WoS

000608437800088

Klíčová slova anglicky

gcType; Global Catalogue of Microorganisms; type strain

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 4. 2. 2021 12:06, Mgr. Marie Šípková, DiS.

Anotace

V originále

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/.

Citovat

SHI, Wenyu, Qinglan SUN, Guomei FAN, Sugawara HIDEAKI, Moriya OHKUMA, Takashi ITOH, Yuguang ZHOU, Man CAI, Song-Gun KIM, Jung-Sook LEE, Ivo SEDLÁČEK, David R. ARAHAL, Teresa LUCENA, Hiroko KAWASAKI, Lyudmila EVTUSHENKO, Bevan S. WEIR, Sarah ALEXANDER, Dlauchy DÉNES, Somboon TANASUPAWAT, Lily EURWILAICHITR, Supawadee INGSRISWANG, Bruno GOMEZ-GIL, Manzour H. HAZBÓN, Marco A. RIOJAS, Chatrudee SUWANNACHART, Su YAO, Peter VANDAMME, Fang PENG, Zenghui CHEN, Dongmei LIU, Xiuqiang SUN, Xinjiao ZHANG, Yuanchun ZHOU, Zhen MENG, Linhuan WU a Juncai MA. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Research. Oxford: Oxford University Press, 2021, roč. 49, D1, s. "D694"-"D705", 12 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaa957.

@article{1718857,
   author = {Shi, Wenyu and Sun, Qinglan and Fan, Guomei and Hideaki, Sugawara and Ohkuma, Moriya and Itoh, Takashi and Zhou, Yuguang and Cai, Man and Kim, SongandGun and Lee, JungandSook and Sedláček, Ivo and Arahal, David R. and Lucena, Teresa and Kawasaki, Hiroko and Evtushenko, Lyudmila and Weir, Bevan S. and Alexander, Sarah and Dénes, Dlauchy and Tanasupawat, Somboon and Eurwilaichitr, Lily and Ingsriswang, Supawadee and GomezandGil, Bruno and Hazbón, Manzour H. and Riojas, Marco A. and Suwannachart, Chatrudee and Yao, Su and Vandamme, Peter and Peng, Fang and Chen, Zenghui and Liu, Dongmei and Sun, Xiuqiang and Zhang, Xinjiao and Zhou, Yuanchun and Meng, Zhen and Wu, Linhuan and Ma, Juncai},
   article_location = {Oxford},
   article_number = {D1},
   doi = {http://dx.doi.org/10.1093/nar/gkaa957},
   keywords = {gcType; Global Catalogue of Microorganisms; type strain},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {gcType: a high-quality type strain genome database for microbial phylogenetic and functional research},
   url = {https://doi.org/10.1093/nar/gkaa957},
   volume = {49},
   year = {2021}
}

TY  - JOUR
ID  - 1718857
AU  - Shi, Wenyu - Sun, Qinglan - Fan, Guomei - Hideaki, Sugawara - Ohkuma, Moriya - Itoh, Takashi - Zhou, Yuguang - Cai, Man - Kim, Song-Gun - Lee, Jung-Sook - Sedláček, Ivo - Arahal, David R. - Lucena, Teresa - Kawasaki, Hiroko - Evtushenko, Lyudmila - Weir, Bevan S. - Alexander, Sarah - Dénes, Dlauchy - Tanasupawat, Somboon - Eurwilaichitr, Lily - Ingsriswang, Supawadee - Gomez-Gil, Bruno - Hazbón, Manzour H. - Riojas, Marco A. - Suwannachart, Chatrudee - Yao, Su - Vandamme, Peter - Peng, Fang - Chen, Zenghui - Liu, Dongmei - Sun, Xiuqiang - Zhang, Xinjiao - Zhou, Yuanchun - Meng, Zhen - Wu, Linhuan - Ma, Juncai
PY  - 2021
TI  - gcType: a high-quality type strain genome database for microbial phylogenetic and functional research
JF  - Nucleic Acids Research
VL  - 49
IS  - D1
SP  - "D694"-"D705"
EP  - "D694"-"D705"
PB  - Oxford University Press
SN  - 03051048
KW  - gcType
KW  - Global Catalogue of Microorganisms
KW  - type strain
UR  - https://doi.org/10.1093/nar/gkaa957
L2  - https://doi.org/10.1093/nar/gkaa957
N2  - 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/.
ER  -

SHI, Wenyu, Qinglan SUN, Guomei FAN, Sugawara HIDEAKI, Moriya OHKUMA, Takashi ITOH, Yuguang ZHOU, Man CAI, Song-Gun KIM, Jung-Sook LEE, Ivo SEDLÁČEK, David R. ARAHAL, Teresa LUCENA, Hiroko KAWASAKI, Lyudmila EVTUSHENKO, Bevan S. WEIR, Sarah ALEXANDER, Dlauchy DÉNES, Somboon TANASUPAWAT, Lily EURWILAICHITR, Supawadee INGSRISWANG, Bruno GOMEZ-GIL, Manzour H. HAZBÓN, Marco A. RIOJAS, Chatrudee SUWANNACHART, Su YAO, Peter VANDAMME, Fang PENG, Zenghui CHEN, Dongmei LIU, Xiuqiang SUN, Xinjiao ZHANG, Yuanchun ZHOU, Zhen MENG, Linhuan WU a Juncai MA. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2021, roč.~49, D1, s.~''D694''-''D705'', 12 s. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaa957.

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