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

Anthony Fullam; Ivica Letunic; Thomas S.B. Schmidt; Quinten R. Ducarmon; Nicolai Karcher; Supriya Khedkar; Michael Kuhn; Martin Larralde; Oleksandr M. Maistrenko; Lukas Malfertheiner; Alessio Milanese; Joao Frederico Matias Rodrigues; Claudia Sanchis-López; Christian Schudoma; Damian Szklarczyk; Shinichi Sunagawa; Georg Zeller; Jaime Huerta-Cepas; Christian Von Mering; Peer Bork; Daniel R. Mende

doi:10.1093/nar/gkac1078

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

Anthony Fullam
, Ivica Letunic
, Thomas S.B. Schmidt
, Quinten R. Ducarmon
, Nicolai Karcher
, Supriya Khedkar
, Michael Kuhn
, Martin Larralde
, Oleksandr M. Maistrenko
, Lukas Malfertheiner
, Alessio Milanese
, Joao Frederico Matias Rodrigues
, Claudia Sanchis-López
, Christian Schudoma
, Damian Szklarczyk
, Shinichi Sunagawa
, Georg Zeller
, Jaime Huerta-Cepas
, Christian Von Mering
, Peer Bork

Daniel R. Mende

European Molecular Biology Laboratory
Biobyte Solutions
Royal Netherlands Institute for Sea Research - NIOZ
University of Zurich
Swiss Federal Institute of Technology Zurich
Technical University of Madrid
Max Delbrück Center for Molecular Medicine in the Helmholtz Association
University of Würzburg
Yonsei University
Amsterdam University Medical Centers

Research output: Contribution to journal › Article › peer-review

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/

Original language	English
Pages (from-to)	D760-D766
Journal	Nucleic Acids Research
Volume	51
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkac1078
Publication status	Published - 6 Jan 2023
Externally published	Yes

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Fullam, A., Letunic, I., Schmidt, T. S. B., Ducarmon, Q. R., Karcher, N., Khedkar, S., Kuhn, M., Larralde, M., Maistrenko, O. M., Malfertheiner, L., Milanese, A., Rodrigues, J. F. M., Sanchis-López, C., Schudoma, C., Szklarczyk, D., Sunagawa, S., Zeller, G., Huerta-Cepas, J., Von Mering, C., ... Mende, D. R. (2023). proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Research, 51(D1), D760-D766. https://doi.org/10.1093/nar/gkac1078

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title = "proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes",

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/",

author = "Anthony Fullam and Ivica Letunic and Schmidt, \{Thomas S.B.\} and Ducarmon, \{Quinten R.\} and Nicolai Karcher and Supriya Khedkar and Michael Kuhn and Martin Larralde and Maistrenko, \{Oleksandr M.\} and Lukas Malfertheiner and Alessio Milanese and Rodrigues, \{Joao Frederico Matias\} and Claudia Sanchis-L{\'o}pez and Christian Schudoma and Damian Szklarczyk and Shinichi Sunagawa and Georg Zeller and Jaime Huerta-Cepas and \{Von Mering\}, Christian and Peer Bork and Mende, \{Daniel R.\}",

note = "Publisher Copyright: {\textcopyright} 2023 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.",

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month = jan,

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doi = "10.1093/nar/gkac1078",

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Fullam, A, Letunic, I, Schmidt, TSB, Ducarmon, QR, Karcher, N, Khedkar, S, Kuhn, M, Larralde, M, Maistrenko, OM, Malfertheiner, L, Milanese, A, Rodrigues, JFM, Sanchis-López, C, Schudoma, C, Szklarczyk, D, Sunagawa, S, Zeller, G, Huerta-Cepas, J, Von Mering, C, Bork, P & Mende, DR 2023, 'proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes', Nucleic Acids Research, vol. 51, no. D1, pp. D760-D766. https://doi.org/10.1093/nar/gkac1078

TY - JOUR

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AU - Fullam, Anthony

AU - Letunic, Ivica

AU - Schmidt, Thomas S.B.

AU - Ducarmon, Quinten R.

AU - Karcher, Nicolai

AU - Khedkar, Supriya

AU - Kuhn, Michael

AU - Larralde, Martin

AU - Maistrenko, Oleksandr M.

AU - Malfertheiner, Lukas

AU - Milanese, Alessio

AU - Rodrigues, Joao Frederico Matias

AU - Sanchis-López, Claudia

AU - Schudoma, Christian

AU - Szklarczyk, Damian

AU - Sunagawa, Shinichi

AU - Zeller, Georg

AU - Huerta-Cepas, Jaime

AU - Von Mering, Christian

AU - Bork, Peer

AU - Mende, Daniel R.

PY - 2023/1/6

Y1 - 2023/1/6

N2 - 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/

AB - 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/

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DO - 10.1093/nar/gkac1078

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JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

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

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