Earth BioGenome Project: Sequencing life for the future of life
Open accessAbstract
Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet’s organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project’s goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.
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Thousands of newly sequenced chromosome-scale genomes are rapidly filling phylogenetic gaps of animal diversity.
“thousands of newly sequenced chromosome-scale genomes are rapidly filling phylogenetic gaps of animal diversity”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [4]
In Project Goals and Anticipated Outcomes (page not available), the paper says that as of October 2017 only 2,534 eukaryotic species had sequenced genomes, only 25 met its reference-genome standard, and reference-quality assemblies were phylogenetically skewed. The 10-Year Road Map (page not available) proposes chromosome-scale assemblies across approximately 9,000 eukaryotic families as a future goal, rather than reporting thousands of newly sequenced animal genomes already filling phylogenetic gaps. (LLM, conf=0.87)
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Experimental — accuracy not yet measuredTOGA provides a general strategy to cope with the annotation and orthology inference bottleneck.
“With the tree of life becoming more densely populated with genomes, thanks to great efforts of large-scale projects and numerous laboratories (26–28, 39), TOGA provides a general strategy to cope with the annotation and orthology inference bottleneck.”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [39]
The Vertebrate Genomes Project, Genome 10K, and Earth BioGenome Project aim to release thousands of new, high-quality genome assemblies over the next decade.
“The Vertebrate Genomes Project38 led by the Genome 10K39 and the Earth BioGenome Project40, among others, aim to release thousands of new, high-quality genome assemblies over the next decade.”
From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [40]
Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to long-read sequencing technologies, DNA proximity ligation sequencing techniques, and genome sequencing consortia.
“Genome sequencing and assembly have become increasingly affordable and computationally tractable thanks to the development of long-read sequencing technologies like the Pacific Biosciences and Oxford Nanopore platforms (52); the development of DNA proximity ligation sequencing techniques, like Hi-C, for genome scaffolding (53–55); and the efforts of genome sequencing consortia (1, 2, 4, 56)”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [4]
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Cites
Ceballos, G., Ehrlich, P. R., & Dirzo, R. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1704949114 · Cited by 2,663 · see citing works
Contentious relationships in phylogenomic studies can be driven by a handful of genes
Shen, X.-X., Hittinger, C. T., & Rokas, A. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0126 · Cited by 520 · see citing works
Ro, D.-K., Ouellet, M., Paradise, E. M., Burd, H., Eng, D., Paddon, C. J., Newman, J. D., & Keasling, J. D. (2008) · BMC Biotechnology · doi:10.1186/1472-6750-8-83 · Cited by 197 · see citing works
Reference-assisted chromosome assembly
Kim, J., Larkin, D. M., Cai, Q., Asan, Zhang, Y., Ge, R.-L., Auvil, L., Capitanu, B., Zhang, G., Lewin, H. A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1220349110 · Cited by 128 · see citing works
Self-citationTelepresence is a potentially transformative tool for field science
Marlow, J., Borrelli, C., Jungbluth, S. P., Hoffman, C., Marlow, J., Girguis, P. R., the AT-36 Team, Dekas, A., Skarke, A., Blackman, D., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1703514114 · Cited by 15 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- Wadman M (2013) Economic return from Human Genome Project grows. Nature, 10.1038/nature.2013.13187. · DOI
- Droege G, et al. (2016) The Global Genome Biodiversity Network (GGBN) data standard specification. Database (Oxford) 2016:baw125.
- Novak AM, et al. (2017) Genome graphs. bioRxiv:10.1101/101378. · DOI
Cited by
Sorted by citations
Sensitive protein alignments at tree-of-life scale using DIAMOND
Buchfink, B., Reuter, K., & Drost, H.-G. (2021) · Nature Methods · doi:10.1038/s41592-021-01101-x · Cited by 5,097 · see citing works
Cunningham, F., Achuthan, P., Akanni, W., Allen, J., Amode, M. R., Armean, I. M., Bennett, R., Bhai, J., Billis, K., Boddu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1113 · Cited by 925 · see citing works
Population genomics for wildlife conservation and management
Hohenlohe, P. A., Funk, W. C., & Rajora, O. P. (2021) · Molecular Ecology · doi:10.1111/mec.15720 · Cited by 702 · see citing works
Progressive Cactus is a multiple-genome aligner for the thousand-genome era
Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2871-y · Cited by 586 · see citing works
Self-citationNanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0503-6 · Cited by 567 · see citing works
Self-citationFrom telomere to telomere: The transcriptional and epigenetic state of human repeat elements
Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., et al. (2022) · Science · doi:10.1126/science.abk3112 · Cited by 411 · see citing works
Genomes OnLine database (GOLD) v.7: updates and new features
Mukherjee, S., Stamatis, D., Bertsch, J., Ovchinnikova, G., Katta, H. Y., Mojica, A., Chen, I.-M. A., Kyrpides, N. C., & Reddy, T. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky977 · Cited by 230 · see citing works
Integrating gene annotation with orthology inference at scale
Kirilenko, B. M., Munegowda, C., Osipova, E., Jebb, D., Sharma, V., Blumer, M., Morales, A. E., Ahmed, A.-W., Kontopoulos, D.-G., Hilgers, L., et al. (2023) · Science · doi:10.1126/science.abn3107 · Cited by 209 · see citing works
Self-citationAlphaFold heralds a data-driven revolution in biology and medicine
Thornton, J. M., Laskowski, R. A., & Borkakoti, N. (2021) · Nature Medicine · doi:10.1038/s41591-021-01533-0 · Cited by 185 · see citing works
The Value of Reference Genomes in the Conservation of Threatened Species
Brandies, P., Peel, E., Hogg, C. J., & Belov, K. (2019) · Genes · doi:10.3390/genes10110846 · Cited by 158 · see citing works
Pearman, W. S., Freed, N. E., & Silander, O. K. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-3528-4 · Cited by 114 · see citing works
Zhou, J., Chen, S., Wu, Y., Li, H., Zhang, B., Zhou, L., Hu, Y., Xiang, Z., Li, Z., Chen, N., et al. (2024) · Science Advances · doi:10.1126/sciadv.adh8601 · Cited by 63 · see citing works
Mao, Y., & Zhang, G. (2022) · Nature Methods · doi:10.1038/s41592-022-01512-4 · Cited by 50 · see citing works
Self-citationOrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability
Emms, D. M., Liu, Y., Belcher, L., Holmes, J., & Kelly, S. (2026) · Nature Methods · doi:10.1038/s41592-026-03126-6 · Cited by 25 · see citing works
Applied genomics for identification of virulent biothreats and for disease outbreak surveillance
Nwadiugwu, M. C., & Monteiro, N. (2023) · Postgraduate Medical Journal · doi:10.1136/postgradmedj-2021-139916 · Cited by 11 · see citing works
Topological Approaches in Animal Comparative Genomics
Schultz, D. T., & Simakov, O. (2026) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-030424-084541 · Cited by 1 · see citing works
Chan, V. S., Mohamed, F. B., Salleh, F. B. M., Iglesias, A., Abdul-Rahman, A., Miga, M., Najjar, F. H., & Cao, C. (2026) · Information Visualization · doi:10.1177/14738716261498353
- Authors
- Lewin, H. A., Robinson, G. E., Kress, W. J., Baker, W. J., Coddington, J., Crandall, K. A., Durbin, R., Edwards, S. V., Forest, F., Gilbert, M. T. P., Goldstein, M. M., Grigoriev, I. V., Hackett, K. J., Haussler, D., Jarvis, E. D., Johnson, W. E., Patrinos, A., Richards, S., Castilla-Rubio, J. C., van Sluys, M.-A., Soltis, P. S., Xu, X., Yang, H., & Zhang, G.
- Affiliations
- Institute of the Environment (US)
- University of Illinois Urbana-Champaign (US)
- Smithsonian Institution (US)
- Royal Botanic Gardens, Kew (GB)
- Milken Institute (US)
- University of Cambridge (GB)
- Harvard University (US)
- University of Copenhagen (DK)
- George Washington University (US)
- Joint Genome Institute (US)
- Beltsville Agricultural Research Center (US)
- Howard Hughes Medical Institute (US)
- Rockefeller University (US)
- University of California, Santa Barbara (US)
- Baylor College of Medicine (US)
- World Economic Forum (CH)
- Departmento de Botanica, Instituto de Biociencia, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil;
- Florida Museum of Natural History (US)
- BGI Group (China) (CN)
- ORCID
- Lewin, Harris A.
- Robinson, Gene E.
- Kress, W. John
- Baker, William J.
- Coddington, Jonathan
- Crandall, Keith A.
- Durbin, Richard
- Edwards, Scott V.
- Forest, Félix
- Gilbert, M. Thomas P.
- Goldstein, Melissa M.
- Grigoriev, Igor V.
- Hackett, Kevin J.
- Haussler, David
- Jarvis, Erich D.
- Johnson, Warren E.
- Richards, Stephen
- Soltis, Pamela S.
- Xu, Xun
- Yang, Huanming
- Zhang, Guojie
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2018-04-23
- Volume
- 115
- Issue
- 17
- Pages
- 4325-4333
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC5924910
- OpenAlex
- W2802282671
- Cited by
- 962
- References
- 5
- Citations by year
- 2026: 106 · 2025: 108 · 2024: 114 · 2023: 128 · 2022: 160 · 2021: 147 · 2020: 98 · 2019: 70 · 2018: 29 · 2012: 2
- FWCI
- 30.74
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Howard Hughes Medical Institute
- Wellcome Trust (207492/Z/17/Z)
- Lundbeckfonden (R190-2014-2827)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- Earth BioGenome Project, Nagoya Protocol, access and benefit sharing, international scientific collaboration, biodiversity conservation, climate change impacts on biodiversity, ecosystem services
- MeSH terms
- Genome, Earth, Planet, Biodiversity, Endangered Species, High-Throughput Nucleotide Sequencing
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