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:https://doi.org/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 BorkDaniel R. Mende

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

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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

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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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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/",

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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

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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.

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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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JF - Nucleic Acids Research

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

Abstract

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