Abstract
The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Ebenezer, T. E. et al. Africa: sequence 100,000 species to safeguard biodiversity. Nature 603, 388–392 (2022).
Sharaf, A. et al. Bridging the gap in African biodiversity genomics and bioinformatics. Nat. Biotechnol. 41, 1348–1354 (2023).
Lewin, H. A. et al. The Earth BioGenome Project 2020: starting the clock. Proc. Natl Acad. Sci. USA 119, e2115635118 (2022).
Heuertz, M. et al. The application gap: genomics for biodiversity and ecosystem service management. Biol. Conserv. 278, 109883 (2023).
Theissinger, K. et al. How genomics can help biodiversity conservation. Trends Genet. 39, 545–559 (2023).
Moore, B. et al. Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries. PLoS Comput. Biol. 17, e1009218 (2021).
Bandara, S. et al. Imagining a future in global health without visa and passport inequities. PLOS Glob. Public Health 3, e0002310 (2023).
Mulder, N. J. et al. The development of computational biology in South Africa: successes achieved and lessons learnt. PLoS Comput. Biol. 12, e1004395 (2016).
Ras, V. et al. Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa. PLoS Comput. Biol. 17, e1008640 (2021).
BecA-ILRI Hub. BecA-ILRI Hub 2017 Annual Report: Unlocking Agricultural Prosperity in Africa cgspace.cgiar.org/server/api/core/bitstreams/ad8685bb-26f6-4018-b99f-4f78b1c9b0e7/content (International Livestock Research Institute, 2018).
Makhalanyane, T. P. et al. African microbiomes matter. Nat. Rev. Microbiol. 21, 479–481 (2023).
Bennis, M. et al. Plant growth promoting activities of Pseudomonas sp. and Enterobacter sp. isolated from the rhizosphere of Vachellia gummifera in Morocco. FEMS Microbiol. Ecol. 99, fiad114 (2023).
Hirsch, A. A strategic consideration of the African Union Free Movement of Persons Protocol and other initiatives towards the freer movement of people in Africa. www.jstor.org/stable/resrep29589 (2021).
Inzaule, S. C., Tessema, S. K., Kebede, Y., Ogwell Ouma, A. E. & Nkengasong, J. N. Genomic-informed pathogen surveillance in Africa: opportunities and challenges. Lancet Infect. Dis. 21, e281–e289 (2021).
Herbert, D. L., Barnett, A. G., Clarke, P. & Graves, N. On the time spent preparing grant proposals: an observational study of Australian researchers. BMJ Open 3, e002800 (2013).
Parrilla, J. M. ChatGPT use shows that the grant-application system is broken. Nature 623, 443 (2023).
Li, Q., Ge, Y. & Sayer, J. A. Challenges to implementing the Kunming–Montreal global biodiversity framework. Land 12, 2166 (2023).
Obura, D. The Kunming–Montreal Global Biodiversity Framework: business as usual or a turning point? One Earth 6, 77–80 (2023).
Smith, D., Ryan, M. J. & Buddie, A. G. The Role of Digital Sequence Information in the Conservation and Sustainable Use of Genetic Resources for Food and Agriculture: Opportunities and Challenges Background Study Paper No. 73 (Commission on Genetic Resources for Food and Agriculture, Food and Agriculture Organization, 2023).
Serwadda, D., Ndebele, P., Grabowski, M. K., Bajunirwe, F. & Wanyenze, R. K. Open data sharing and the Global South—who benefits? Limited capacity, deep mistrust pose challenges to sharing. Science 359, 642–643 (2018).
Hutson, M. The race to save the world’s DNA. The New Yorker www.newyorker.com/science/elements/the-race-to-save-the-worlds-dna (2023).
Lee, B. et al. Introduction of the Korea BioData Station (K-BDS) for sharing biological data. Genomics Inform. https://doi.org/10.5808/gi.22073 (2023).
Mitchell, P. K. et al. Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria. Microb. Genom. https://doi.org/10.1099/mgen.0.000717 (2022).
Cycil, L. M. et al. Metagenomic insights into the diversity of halophilic microorganisms indigenous to the Karak salt mine, Pakistan. Front. Microbiol. 11, 1567 (2020).
Hon, T. et al. Highly accurate long-read HiFi sequencing data for five complex genomes. Sci. Data 7, 399 (2020).
Kim, C., Pongpanich, M. & Porntaveetus, T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J. Transl. Med. 22, 111 (2024).
Shirasawa, K., Kobayashi, N., Nakatsuka, A., Ohta, H. & Isobe, S. Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense. DNA Res. https://doi.org/10.1093/dnares/dsab010 (2021).
Player, R. et al. Optimization of Oxford Nanopore Technology sequencing workflow for detection of amplicons in real time using ONT-DART tool. Genes (Basel) https://doi.org/10.3390/genes13101785 (2022).
Chapman, R. et al. Nanopore-based metagenomic sequencing in respiratory tract infection: a developing diagnostic platform. Lung 201, 171–179 (2023).
Latorre-Pérez, A., Villalba-Bermell, P., Pascual, J. & Vilanova, C. Assembly methods for nanopore-based metagenomic sequencing: a comparative study. Sci. Rep. 10, 13588 (2020).
Liu, L., Yang, Y., Deng, Y. & Zhang, T. Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes. Microbiome 10, 209 (2022).
Tenaillon, O. et al. Tempo and mode of genome evolution in a 50,000-generation experiment. Nature 536, 165–170 (2016).
Wynberg, R. & Chennells, R. in Indigenous Peoples, Consent and Benefit Sharing: Lessons from the San–Hoodia Case (eds Wynberg, R. et al.) 89–124 (Springer, 2009).
Cherry, M. South Africa—serious about biodiversity science. PLoS Biol. 3, e145 (2005).
Secretariat of the Convention on Biological Diversity. Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity www.cbd.int/abs/doc/protocol/nagoya-protocol-en.pdf (United Nations, 2011).
Secretariat of the Convention on Biological Diversity. Convention on Biological Diversity www.cbd.int/doc/legal/cbd-en.pdf (United Nations, 2011).
Commission on Genetic Resources for Food and Agriculture. Global Plan of Action for Animal Genetic Resources and the Interlaken Declaration www.fao.org/3/a1404e/a1404e.pdf (Food and Agriculture Organization of the United Nations, 2007).
Ahmad, M. 3. Trade in endangered species. Yearb. Int. Environ. Law 31, 121–124 (2020).
Challender, D. W. S. et al. Identifying species likely threatened by international trade on the IUCN Red List can inform CITES trade measures. Nat. Ecol. Evol. 7, 1211–1220 (2023).
Folarin, O. A., Happi, A. N. & Happi, C. T. Empowering African genomics for infectious disease control. Genome Biol. 15, 515 (2014).
Tateno, Y. & Gojobori, T. DNA Data Bank of Japan in the age of information biology. Nucleic Acids Res. 25, 14–17 (1997).
Stoesser, G. et al. The EMBL nucleotide sequence database. Nucleic Acids Res. 26, 8–15 (1998).
Smith, K. A Brief History of NCBI’s Formation and Growth www.ncbi.nlm.nih.gov/books/NBK148949/ (National Center for Biotechnology Information, 2013).
Arita, M., Karsch-Mizrachi, I. & Cochrane, G. The international nucleotide sequence database collaboration. Nucleic Acids Res. 49, D121–D124 (2021).
Kuster, R. D., Yencho, G. C. & Olukolu, B. A. ngsComposer: an automated pipeline for empirically based NGS data quality filtering. Brief. Bioinform. 22, bbab092 (2021).
Bredeson, J. V. et al. Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Nat. Commun. 13, 2001 (2022).
Wellcome Trust. Beyond the sequence: ethical, legal and social contexts in genomics. wellcome.org/what-we-do/our-work/beyond-sequence-ethical-legal-and-social-contexts-genomics (2023).
Caelers, D. & Okoth, D. Research funding in Africa: navigating sustainability and shifting perspectives. Nat. Afr. https://doi.org/10.1038/D44148-023-00360-4 (2023).
Cerdeira, J., Mesquita, J. & Vieira, E. S. International research collaboration: is Africa different? A cross-country panel data analysis. Scientometrics 128, 2145–2174 (2023).
United Nations Conference on Trade and Development. Technology and Innovation Report 2021 https://unctad.org/system/files/official-document/tir2020_en.pdf (United Nations, 2021).
Acknowledgements
We would like to thank all listed partners and sponsors (Fig. 2) who made the 2023 series of the AfricaBP Open Institute regional workshops possible, as well as G. E. Robinson, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA, for reviewing the initial draft of the manuscript. The African Genome Center (AGC)–AfricaBP Open Institute Fellowship is funded by grant number AS-77 from the Office Chérifien des Phosphates Group and the University Mohammed VI Polytechnic in Morocco awarded to the AGC.
Author information
Authors and Affiliations
Contributions
Conceived and initiated the regional workshops: T.E.E. and J.O.O. Designed the regional workshop model: J.O.O. and T.E.E. Discussed the designed model and implemented and executed the regional workshops: T.E.E., J.O.O., N.M., B.B., A.M., L.T.N., I. Hayah, J.O.K., S. Mdyogolo, T.C.O., B.A.O., R.M.S, A. Barakat, A.M.M., A.E.H., A. Benkahla, A. Boukteb, A.E., A.L.M., A.M.A., A.K.E., B.A., C.W., C.C.N., C.E., D.I., E.E.F., E.A., F.O., F.Z.B., F.Z.T., F.R., F.Z., G.L.M., H.G., M. Hanachi, H.N., H.C., I.B., I.M., I. Haddadi, I.M.K., J.F.M., J.-B.K.D.E., J.B.R., J. Ogwang, J.B.D., K.E., K.L., K.K.K., L.B.T., L.H., M.R., M. Chaisi, M.W.B., M. Kilian, M. Kvas, M. Melloul, M. Chaouch, M. Khyatti, M.A., M.P.-M., M. Hijri, M.R.M., M.A.H., M.P., M. Mwale, M. Maaloum, M. Mavhunga, N.A.O., O. Aminou, O. Arbani, O.S., P.F.D., R. Mentag, R.D.Z., R.B.T., R. Megnekou, S.P.K., S.S., S.E., S.B.S.G., S.R.A.R., S.F., S.K., S.A., T.M., T.S., O.U.U., V.E., X.D., Y.G., Y.H.T., Z.C., C.Z. and A.D. Drafted the manuscript: T.E.E., A.S., K.L., J. Ogwang, M.W.B., A. Benkahla, M. Chaouch, X.D., A.M.M., N.A.O., M.P.-M., R.B.T. and V.R. Analyzed data: T.E.E., G.B., A.S. and R.M.S. Reviewed the manuscript: T.E.E., J.O.O., A.M., G.B., C.J.K., D.-F.N., F.B.M., F.R., F.Z., J. Ogwang, J.E.I., K.E., K.K.K., L.B.T., M. Chaouch, M.W.B., M. Hijri, M.P., M. Mwale, R.B.T., S. Muzemil, S.P., S.P.S., S.B.S.G., S.K., O.U.U., V.E., V.C.D., X.D., Z.M.-D., C.H. and T.K. Approved the manuscript: all authors.
Corresponding authors
Ethics declarations
Competing interests
A.M.M. and H.G. are employees of Inqaba Biotechnical Industries. Z.C., M.A., S.E., L.H., T.S. and X.D. are employees of Illumina, Inc. M. Kilian, M. Kvas and C.W. are employees of Separations (Pty) Ltd. M. Maaloum and F.Z.T. are employees of Megaflex. M.P.-M. is an employee of MGI-Tech. R.B.T. is an employee of Inqaba Biotec Central Africa. T.E.E. is an independent contractor for the Wellcome Trust. All other authors declare no competing interests.
Peer review
Peer review information
Nature Genetics thanks Sofonias Tessema and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Supplementary Information
Supplementary Figs. 1–5 and Table 1.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Sharaf, A., Nesengani, L.T., Hayah, I. et al. Establishing African genomics and bioinformatics programs through annual regional workshops. Nat Genet (2024). https://doi.org/10.1038/s41588-024-01807-6
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41588-024-01807-6
