proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes-Reference-Cited by-同舟云学术

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Published:2022-11-21 Issue:D1 Volume:51 Page:D760-D766
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Fullam Anthony¹^ORCID,Letunic Ivica²^ORCID,Schmidt Thomas S B¹^ORCID,Ducarmon Quinten R¹^ORCID,Karcher Nicolai¹^ORCID,Khedkar Supriya¹^ORCID,Kuhn Michael¹^ORCID,Larralde Martin¹^ORCID,Maistrenko Oleksandr M³^ORCID,Malfertheiner Lukas⁴^ORCID,Milanese Alessio⁵^ORCID,Rodrigues Joao Frederico Matias⁴^ORCID,Sanchis-López Claudia⁶^ORCID,Schudoma Christian¹^ORCID,Szklarczyk Damian⁴^ORCID,Sunagawa Shinichi⁵^ORCID,Zeller Georg¹^ORCID,Huerta-Cepas Jaime⁶^ORCID,von Mering Christian⁴^ORCID,Bork Peer¹⁷⁸⁹^ORCID,Mende Daniel R¹⁰^ORCID

Affiliation:

1. Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany

2. Biobyte solutions GmbH , Bothestr. 142, 69117 Heidelberg, Germany

3. Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology & Biogeochemistry , 1797 SZ, ’t Horntje (Texel), Netherlands

4. Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich , 8057 Zurich, Switzerland

5. Institute of Microbiology, Department of Biology and Swiss Institute of Bioinformatics , ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland

6. Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) , Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain

7. Max Delbrück Centre for Molecular Medicine , 13125 Berlin, Germany

8. Department of Bioinformatics, Biocenter, University of Würzburg , 97074 Würzburg, Germany

9. Yonsei Frontier Lab (YFL), Yonsei University , 03722 Seoul, South Korea

10. Department of Medical Microbiology, Amsterdam University Medical Centers , Amsterdam, The Netherlands

Abstract

Abstract The interpretation of genomic, transcriptomic and other microbial ‘omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/

Funder

Amsterdam UMC

European Molecular Biology Laboratory

Swiss National Science Foundation

NCCR Microbiomes

German Federal Ministry of Education and Research

German Research Foundation

European Grant

Spanish Ministry of Universities

Publisher

Oxford University Press (OUP)

Subject