proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands robust quality control and consistent annotation pipelines to ensure meaningful biological insights. proGenomes4 (prokaryotic Genomes v4) addresses this challenge by providing a resource of nearly 2 million high-quality microbial genomes, a doubling in scale from previous versions, encompassing over 7 billion genes. Each genome underwent rigorous quality assessment and comprehensive functional annotation by applying multiple standardized annotation workflows, including the systematic identification of mobile genetic elements and biosynthetic gene clusters. proGenomes4 contains 32 887 species with ecological habitat metadata as well as precomputed pan-genomes. This substantially expanded resource provides the microbiology community with a foundation for large-scale comparative studies and is freely accessible via a newly developed command line interface and at https://progenomes.embl.de/.
Authors
- Oleksandr M. Maistrenko (ORCID: https://orcid.org/0000-0003-1961-7548)
- Anthony Fullam (ORCID: https://orcid.org/0000-0002-0884-8124)
- Daniel R. Mende (ORCID: https://orcid.org/0000-0001-6831-4557)
- Christian Schudoma (ORCID: https://orcid.org/0000-0003-1157-1354)
- Shahriyar Mahdi Robbani (ORCID: https://orcid.org/0000-0003-0161-0559)
- Supriya Khedkar (ORCID: https://orcid.org/0000-0001-6606-2202)
- Thomas Schmidt (ORCID: https://orcid.org/0000-0001-8587-4177)
- Ivica Letunić (ORCID: https://orcid.org/0000-0003-3560-4288)
- Peer Bork (ORCID: https://orcid.org/0000-0002-2627-833X)
- Anastasiia Grekova (ORCID: https://orcid.org/0009-0002-9092-8584)
- Luís Pedro Coelho (ORCID: https://orcid.org/0000-0002-9280-7885)
- Michael Kuhn (ORCID: https://orcid.org/0000-0002-2841-872X)
- A. Castro (ORCID: https://orcid.org/0009-0004-7393-4127)
Institutions
- Netherlands Institute for Neuroscience (NL)
- Translational Research Institute (AU)
- Keio University (JP)
- Max Delbrück Center (DE)
- Heidelberg University (DE)
- University of Würzburg (DE)
- Biobyte Solutions (Germany) (DE)
- European Molecular Biology Laboratory (DE)
- APC Microbiome Institute (IE)
- European Molecular Biology Laboratory (DE)
- Amsterdam University of Applied Sciences (NL)
- Heidelberg University (US)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-11-20
- DOI
- https://doi.org/10.1093/nar/gkaf1208
- Citations
- 1
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- European Molecular Biology Laboratory
- Deutsche Forschungsgemeinschaft
- Keio University
- Ministry of Education, Culture, Sports, Science and Technology
- Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg
- German Network for Bioinformatics Infrastructure