Background

The African BioGenome Project (AfricaBP) (https://africanbiogenome.org/) is a transformative, continent-wide initiative aimed at sequencing, cataloging, and studying the genomes of Africa’s rich and diverse biodiversity. Among its ambitious goals is the sequencing of approximately 105,000 non-human genomes (plants, animals, fungi, protozoa, and other eukaryotes), a crucial endeavor to benefit the African population in areas of food security and biodiversity conservation with the applications of advanced tools of biotechnology and genomics to build a sustainable bioeconomy1. The Open Institute for Genomics and Bioinformatics (Open Institute) is the knowledge exchange platform of the AfricaBP, which was established to enable curriculum development, technology and infrastructure advancements, policy influence, encourage scientific entrepreneurship and enhance bioeconomy through biodiversity genomics and bioinformatics across Africa2,3.

The increasing concern about changing climatic conditions and their effects on the management and conservation of biological resources highlights the urgent need to develop effective models for sustainable resource management4. The bioeconomy is the production, utilization, and conservation of biological resources, including related knowledge, science, technology, and innovation, to provide information, products, processes, and services across all economic sectors, aiming toward a sustainable economy5. It entails, amongst others, the production of renewable biological resources and the conversion of these resources into value-added products4,6. According to the World Bioeconomy Forum, the current total value of the global bioeconomy is estimated at US$4 trillion7,8, encompassing the financial value of products in, amongst others, agriculture, forestry, food, bioenergy, biotechnology and green chemistry, which were exported worldwide9. This value could potentially increase to US$30 trillion by 2050, representing one-third of the global economic value7,8. Currently, the United States of America and North-West Europe lead in bioeconomy research10, with other regions, including Africa, lagging behind.

The bioeconomy is fundamentally dependent on biodiversity7, which provides megadiverse regions such as Africa the opportunities to increase national revenues in a post-fossil economy through genomics advances in generating microbial factories that produce important compounds for the chemical industry11 such as biorefineries12 (Fig. 1). However, of the 17 sectors included in bioeconomy strategies and monitoring across seven (7) countries and the European Union, genomics was notably absent13.

Fig. 1: The proposed 1000 Moroccan genome project will create a positive economic impact and demonstrate an increased cost–benefit ratio.
Fig. 1: The proposed 1000 Moroccan genome project will create a positive economic impact and demonstrate an increased cost–benefit ratio.
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The predicted economic impact and cost–benefit analysis of the genomes project illustrate the projected economic benefits, long-term impacts, and cost–benefit analysis outcomes of the proposed 1000 Moroccan genomes project. A Economic Impact by Sector: shows the distribution of economic impacts across key sectors, including agriculture, fishing, research and development (R&D), education, and other sectors. The largest impacts are observed in agriculture and R&D, respectively, reflecting their central role in generating economic benefits from genome sequencing. The average agricultural contribution is 53% (the total economic impact attributed to agriculture was US$13 million, while the combined impact of all sectors amounted to ~US$24,340,000 million). The average R&D contribution is 40% (the total economic impact for R&D was $10 million, while the same overall economic impact of US$24,340,000 million). B Long-term Economic Impact Projections: illustrate the cumulative economic benefits over a 5-, 10-, and 20-year period. Sectors such as agriculture, R&D, and downstream industries exhibit significant growth, with total impacts surpassing $78 million after 20 years. This underscores the long-term sustainability of the genome sequencing investment. C Cost–benefit Analysis (10-year Projection): displays the results of the 10-year cost-benefit analysis. It highlights key metrics, including Total Cost, Discounted Cost, Total Benefit, Discounted Benefit, and net present value (NPV). The analysis reveals a Benefit–Cost ratio (BCR) of 3.29, indicating that every dollar invested generates US$3.29 in benefits, affirming the economic viability of the project.

In Africa, efforts to implement biotechnology, genomics, bioinformatics, and computational biology such as the Southern African Biosciences Network and Biosciences East and Central Africa are contributing towards the growth of the African bioeconomy ecosystem, but these are variable across countries and regions2,3,14,15,16. For example, an analysis of 152 studies on the African bioeconomy showed South Africa as the leading nation in African bioeconomy research, with strong interconnection to other African geographical regions, followed by the gradual progress of Nigeria, Kenya, Ghana, as well as the slow progress of Tanzania, Ethiopia, Zimbabwe, Botswana, Rwanda, Egypt, and Madagascar17. The findings of the analysis contextualize continental research loopholes such as limited opportunities in prioritizing research and development (R&D) in public policies and strategies, including limited agricultural interventions to address natural resource degradation, climate change18 and limited information on the revenue value of the African bioeconomy19,20 as well as the contributions of biodiversity genomics and bioinformatics to the African bioeconomy1.

The AfricaBP Open Institute is enhancing capacity-building and strengthening efforts across Africa, advancing our knowledge in genomics and bioinformatics and their contributions to the African bioeconomy. For instance, in 2023, the AfricaBP Open Institute organized the inaugural edition of its regional workshop model involving awareness and hands-on practicals in genomics, bioinformatics, sample collections, and policy thematic areas2,3. In 2024, the AfricaBP Open Institute built upon its inaugural regional workshop model by organizing thirty-one (31) workshops through public–private partnerships, which attracted 3595 registered attendees across 50 African countries and trained 401 African researchers (Figs. S1–S4).

Here, we highlight the current understanding of the applications of biodiversity genomics and bioinformatics in driving the African bioeconomy; assess and predict the economic impact of locally sequencing genomes of African endemic and indigenous species and integrating sequencing into national economic plans and bioeconomy strategies; examine the advancements in the AfricaBP Open Institute in 2024 through the development of fellowship programs and its hands-on genomics and bioinformatics practical workshops; and provide actionable strategies for future directions of the AfricaBP Open Institute to drive measurable impacts.

The predicted economic impact of biodiversity genomics on the African bioeconomy: A Moroccan case study

The global genomics market is projected to grow from US$42.64 billion in 2024 to US$66.85 billion by 2029, and it is driven by factors such as increased prevalence of human genetic disorders, rising adoption of personalized medicine, and technological advancements in genome sequencing21. In Africa, the economic impact of genomics and bioinformatics is significant. A cost–benefit analysis of the South African Beef Genomics Program revealed that a total investment of US$44 million over 10 years was expected to yield at least US$139 million in benefits, with an economic return of 18.70% and a Benefit–Cost Ratio of 3.1, indicating that the present value of future benefits would be approximately three times the costs incurred22. However, the genomics economy in Africa faces unique challenges, and it is yet to be maximized23,24. African countries allocate an average of 0.45% of their GDP to R&D25, significantly below the global average of 1.7%26. This underinvestment is largely attributed to insufficient government funding for R&D, infrastructure development, and human capital capacity-building initiatives27. These limitations hinder the transformation of Africa’s intellectual capital into tangible products and services that could boost economic growth28.

Biodiversity genomics offers transformative economic opportunities for Africa, with the sequencing of 105,000 species projected to generate substantial direct, indirect, and induced impacts across the continent. Contributing to these sequenced genomes requires concerted efforts at the national level, especially driven by national networks of scientists in biodiversity genomics and bioinformatics1. Here, we draw insights from Morocco’s proposed 1000 genome sequencing investment model (Fig. 1), highlighting the economic and societal benefits of genome sequencing for the African bioeconomy.

Approaches and outcomes

We performed an economic impact and cost-benefit analysis (see Box 1 for detailed methodology) of sequencing 1000 Moroccan genomes locally in Morocco. To evaluate the economic impacts, an Input/Output (I/O) analysis was conducted using the Leontief I/O model29. This methodology examines economic interdependencies between sectors and quantifies the direct, indirect, and induced effects of investments. The Cost-Benefit Analysis framework assessed the economic feasibility and sustainability of the genome sequencing initiative over a 10-year period, and it involved using the economic metrics derived from I/O model outputs, environmental data, net present value calculations, and key assumptions such as an investment of US$20 million in the proposed 1000 Moroccan genome project. The outcomes show impacts across sectors, long-term projects, and economic returns as described below

  • Sectoral contributions agriculture and beyond

    Genome sequencing directly benefits agriculture, fishing, research and development (R&D), and education (Fig. 1A). Agriculture, the largest contributor, accounts for over 53% of total economic output, driven by innovations like precision breeding of drought-resistant crops and disease-resilient livestock. These advancements improve yields and food security, especially for biodiversity-rich nations suchas Kenya and Madagascar30,31. Fishing and aquaculture also benefit through sustainable practices and resilient species identification (Fig. 1A). Meanwhile, R&D catalyzes innovation across agriculture, pharmaceuticals, and conservation, contributing 40% of economic returns (Fig. 1A). Educational investments ensure a skilled workforce capable of implementing these genomic advancements.

  • Long-term projections

    The economic benefits of genome sequencing are projected to grow significantly over time (Fig. 1B). Over two decades, total economiccontributions are expected to rise from US$35 million in the first 5 years to US$79 million by the 20th year. Agriculture remains thedominant sector, reaching US$34 million by the 20th year, while R&D maintains a steady 28% contribution. Spillover benefits fromagriculture bolster downstream industries like food processing and ecotourism, collectively adding millions to Africa’s economy (Fig. 1B).

  • Cost-effectiveness: Strong economic returns

    A cost-benefit analysis highlights the initiative’s economic feasibility, with a Benefit–Cost Ratio (BCR) of 3.29, indicating US3.29 in benefits for every US$1 invested (Fig. 1C). Over 10 years, a $20 million investment is projected to yield discounted benefits of US$40 million and a net present value (NPV) of US$28 million (Fig. 1C).

Integrating genomics and bioinformatics into national economic plans and bioeconomy strategies

To fully harness the transformative potential of biodiversity genomics, African countries and institutions should adopt a strategic and integrative economic approach. Establishing regional sequencing hubs and state-of-the-art laboratories is critical to reducing dependency on external facilities, fostering local innovations, and providing jobs for early careers and established scientists32,33. Simultaneously, capacity-building initiatives should be strengthened through comprehensive training programs and international partnerships to equip a skilled workforce with the expertise needed to implement genomic technologies effectively2,3. Prioritizing the sequencing of high-impact species, such as drought-resistant crops and disease-resilient livestock, will ensure maximum economic, environmental, and societal benefits34. Furthermore, robust policies must be developed to safeguard genomic data, promote equitable sharing of benefits, and protect intellectual property derived from genomic research35. Encouraging public–private partnerships through incentives like tax breaks and grants will attract investments and enable collaboration between governments, academia, and industries36.

The landscape of national bioeconomy strategies across Africa

African nations are increasingly adopting bioeconomy strategies to govern biodiversity for sustainable development, addressing gaps in education, R&D, and policymaking17. Only 12 African countries have established bioeconomy strategies: South Africa and Ethiopia have comprehensive bioeconomy strategies37,38, while Senegal, Nigeria, Ghana, Mali, Kenya, Mauritius, Mozambique, Namibia, Tanzania, and Uganda have bioeconomy-related strategies37.

South Africa is a continental leader in the bioeconomy, integrating agriculture, health, and industry within its bioeconomy framework through institutions like the Technology Innovation Agency and significant public-private investments39,40. Notably, sustainable marine aquaculture has become an emerging component of this food security and economic growth strategy, aligning with broader national goals to diversify the blue economy and improve nutrition, employment, and livelihoods through aquaculture innovation41,42. One example is the application of genomic techniques such as quantitative trait loci (QTL) mapping and genome annotation to improve growth, disease resistance, and productivity in key aquaculture species like abalone (Haliotis midae)43,44. Genomic studies on Cape hakes also reveal population structure shaped by overfishing, prompting region-specific management45,46. These efforts are supported by regional initiatives such as ASTRAL and LIMAQUA, which promote the integration of genomics into sustainable aquaculture practices across Africa47,48. Collectively, these initiatives have positioned the country as a global bioeconomy model, supported by strong policies and infrastructure39.

Similarly, within the Southern African region, Namibia links its bioeconomy development strategy to its Vision 2030 by focusing on biomass from bush thinning for job creation, biodiversity management, and sustainable land use, all established by multi-stakeholder engagement17,39,40. In East Africa, the 2022 modern bioeconomy strategy by the East African Community, which includes Burundi, Kenya, Rwanda, South Sudan, Tanzania, and Uganda, has significant potential to support several critical development goals and targets for the region. This strategy aimed at creating an enabling environment for increased Science, Technology, and Innovation (STI) investments to support sustainable development and socio-economic transformation49. For instance, Uganda has particularly focused its bioeconomy development strategy on advancing its agricultural and energy sectors through biotechnology and nanotechnology, and also on promoting public-private partnerships39,40. Furthermore, Ethiopia has recently implemented a national bioeconomy strategy to benefit from its rich diversity of flora and fauna through the development and promotion of a sustainable knowledge-based bioeconomy38.

In West Africa, Nigeria aligns its bioeconomy initiatives with its national biotechnology policy (2001) and the biofuel policy incentives (2007)20, while Ghana aligns with the Climate-Smart Agriculture Plan39, respectively. Ghana capitalizes on its rich biodiversity and biomass resources to promote economic growth, including the development of sustainable bio-manufacturing industries40. Moreover, educational institutions and public–private partnerships play a central role in driving Ghana’s science and technology outputs for economic growth50.

Current understanding of African bioeconomy through biodiversity genomics

The AfricaBP Open Institute regional workshops in 2024 were organized using the model previously discussed in Sharaf et al.3, over a 5-day period. Days 1 and 2 were symposium style (Fig. S1) which recorded a total of 3595 registered attendees (Figs. S2–S4) while Day 3–5 were distributed practicals across multiple sites and countries. The regional workshops were coordinated by the University of Port Harcourt, Nigeria (West Africa) from 5 to 9 May, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Kenya (East and Central Africa) from 5 to 9 August, University of South Africa (Southern Africa), from 9th to 13th September, and Mohammed V University in Rabat (UM5R), Morocco (North Africa) from 25 to 29 November, respectively. Here, we provide a synthetic review of selected keynotes, guests, oral and poster presentations by early career and established researchers during Day 1 and Day 2 across all five African geographical regions, and these are categorized under the five AfricaBP Grand Challenges1,2 as given below.

  • Genomics and bioinformatics technologies for the agri-environment

    Recent advancements in genomics and bioinformatics have the potential to revolutionize agriculture, livestock management, and biodiversity conservation51,52. For instance, progress in sequencing technologies, particularly long-read sequencing methods, has addressed challenges in genome assembly, enabling near error-free reference genomes that significantly enhance the accuracy of functional genomic analyses53.

    Furthermore, the generation of high-quality genome assemblies for African cattle breeds, namely: Bos indicus × Bos taurus Mpwapwa, Bos indicus Iringa Red, Bos indicus Singida White, Bos indicus Gudali, and Bos taurus Lagune, represent a significant step forward towards understanding the genetic diversity and adaptive traits underlying Africa’s extensive cattle heritage54,55,56. These assemblies provide resources for identifying genetic markers linked to selection signatures and adaptive expression quantitative trait loci (eQTLs)57. Moreover, they facilitate the development of breeding programs designed to enhance climate resilience and disease resistance, ensuring sustainable livestock systems for the continent58,59.

    The applications extend beyond livestock genomics. The genome assembly of Hippobosca camelina, commonly known as the camel ked, revealed chemosensory genes that are vital to its parasitic lifecycle, enabling targeted control strategies to mitigate economic losses in camel-rearing communities60. Similarly, biodiversity research utilizes genomic tools, with DNA barcoding successfully resolving hidden species within the Labeobarbus genus, advancing both conservation efforts and sustainable fisheries management61.

  • Crops and livestock improvements and health

    Africa is making significant advancements in genomics and innovation to enhance agricultural productivity and address challenges in crop and livestock health for food security. These advancements are evident in several initiatives such as the West African Virus Epidemiology (WAVE) program in Ivory Coast, a collaborative effort being conducted across 10 West and Central African countries62, illustrating the power of genomic surveillance in managing plant pathogens and controlling the spread of exotic diseases63. In Nigeria, genetic studies on rice have identified key traits linked to yield stability and environmental resilience, achieved through marker-assisted backcrossing64. This progress is mirrored in other African contexts, such as in Morocco, where the exploration of Argania spinosa has led to valuable understanding of functional genes involved in oil quality and stress resistance65. Similarly in Ethiopia, comprehensive genomic analyses of sorghum are revealing key genetic loci associated with the development of robust root systems, a critical adaptation for drought tolerance66. These advancements extend beyond crop species. In Tanzania, dairy cows are demonstrating enhanced resilience to high temperatures, which is due to the identification of genetic markers associated with thermal tolerance through genomic studies67. Furthermore, in Morocco, the genetic makeup of the local Sardi sheep breed is characterized, enabling the development of targeted breeding programs that meet the specific needs of local livestock producers68,69. Additionally, research from Morocco highlights the important role of both neutral and adaptive genomic diversity in providing resilience to environmental pressures, laying the groundwork for sustainable breeding programs70,71. The integration of genomics with Artificial intelligence technologies is being actively applied in breeding programs, aiming to enhance food security by prioritizing biodiversity, improving resilience, and optimizing agricultural practices72.

  • Genomics for the conservation of endangered and endemic species

    Over 90% of endangered, endemic, and indigenous African species remain unsequenced, despite their ecological importance and declining populations1. Genomic research on endemic and endangered African species provides important understanding for their preservation and conservation across Africa73. For instance, genomic analyses of African wildlife have demonstrated how disruptions in migratory routes and introgression events shape population structures and phylogeography74,75. Another example is the employment of DNA barcoding techniques by the South African National Biodiversity Institute (SANBI) at the Pretoria National Botanical Gardens to protect South Africa’s biodiversity hotspot76. Advanced methods such as remote sensing and machine learning, are used to study plant phenology, including flowering patterns and their associations with insect pollinators77. Additionally, studies using Malaise traps in cultivated and natural areas are used to reveal variations in insect diversity, while Natural Language Processing techniques have been applied to classify insect functional groups, enhancing the understanding of plant–insect interactions and their ecological significance78.

    Furthermore, the Institute of Genomics and Global Health (IGH, formerly the African Centre of Excellence for Genomics of Infectious Diseases—ACEGID) at Redeemer’s University, Nigeria, employs genomic techniques to address microbial threats in West Africa. This includes the use of real-time genomic sequencing during outbreaks, as evidenced during the Ebola and COVID-19 epidemics79,80. Notable advancements include the development of a multiplex testing platform capable of detecting up to 49 pathogen species in a single test and genome-wide association studies (GWAS), identifying genes linked to resistance and susceptibility to diseases like Lassa fever81. These efforts enhance health crisis management and mitigate risks to both human and wildlife populations. Genomic tools also facilitate the identification of cryptic species, including those critically endangered82. Understanding adaptive traits provides opportunities for timely interventions during disease outbreaks, population declines, or the emergence of invasive species. For example, research on giraffe populations identified significant genetic differentiation and historical gene flow among lineages, challenging traditional species classifications and enriching our understanding of their evolutionary history83. These diverse applications of genomics enable the monitoring of species populations and their health, driving the development of targeted conservation strategies, therefore, preserving Africa’s unique genetic resources and ecological heritage84,85,86.

  • Ethics, socio-economics, and policy issues

    Africa, the world’s second most biodiverse continent87, holds immense potential for aligning biodiversity conservation with socio-economic development, thereby advancing towards a green and blue economy88,89. Preserving ecological infrastructure is crucial for maintaining ecosystem services and reducing reliance on built infrastructure. For example, South Africa’s healthy catchments are vital for water resource management, indicating the significance of ecological health in ensuring resource resilience90. Similarly, Nigeria’s National Biosafety Management Agency (NBMA) reinforces its commitment to safeguarding biodiversity through the responsible application of modern biotechnology91.

    Global frameworks, such as the Kunming–Montreal Global Biodiversity Framework adopted by the Convention on Biological Diversity92, and supported by the International Union for Conservation of Nature (IUCN), offer structured pathways to halt and reverse biodiversity loss and integrate conservation into global policy, focusing on biodiversity preservation and the enhancement of ecosystem services for present and future generations93.

    Data-driven strategies are equally important; the Global Biodiversity Information Facility (GBIF), for instance, mobilizes extensive biodiversity records to provide open access to data, empowering policymakers and researchers to design sustainable, evidence-based practices94. African organizations and programs such as the Nigerian Conservation Foundation contribute to (and leverage on) the GBIF platform to promote sustainable practices in agriculture, forestry, and fisheries, while quantifying the bioeconomy across the region95 and supporting IUCN’s agenda. This approach strengthens Africa’s bioeconomy by advancing biodiversity informatics and guiding policies that promote sustainable resource use96.

    Efforts to promote sustainable landscape connectivity, such as those in the Maghreb region of North Africa, driven by UNESCO, enhance ecosystem resilience while providing socio-economic benefits like improved livelihoods and climate adaptation. Ethical governance and inclusive policies are central to these initiatives97,98.

    Collectively, these initiatives, integrating cultural and biological diversity into science and education, align with the AfricaBP Open Institute’s local-first, global-later strategy. This strategy is founded on regional training, improved data sharing, and inclusive policy advocacy1,2,3 and prioritizes the incorporation of local ethics and socio-economic policies within international discourse2, thereby advancing Africa towards a sustainable path for biodiversity and socio-economic management.

  • Technology development, knowledge exchange, industry, and commercialization

    Many sectors, such as agriculture, construction, food, and beverage, rely on resources from the ecosystem, with a decline in the ecosystem functionality estimated to cost the global economy more than US$5 trillion a year99. Opportunities exist to innovate around conservation, restoration, and building for resilience, integrating genomics, computing, and engineering. The Woolly Mammoth de-extinction project supported by Colossal aims at restoring Alaska’s forests by assessing the extent to which contemporary Arctic ecosystems are conducive to the rewilding of megaherbivores, using a woolly mammoth (Mammuthus primigenius) proxy as a model species through CRISPR-Cas9100, is one such example, and its economic impact is likely to be felt in the recreational sector101. In Africa, similar efforts could aim to restore ecological balance and biodiversity, which, in turn, drive sustainable industries and stimulate economic growth. For example, biodiversity conservation contributes to food security through pollinators, helps stamp out disease reservoirs, and supports medicinal innovations, such as anticancer drugs102,103. The protection of endemic species through strong intellectual property frameworks is also evolving across Africa. Such frameworks allow for the commercialization of genetic resources, protect local innovations, and encourage investments in the bioeconomy, especially since intellectual property protection is mandatory in facilitating open science practices, promoting collaboration, and enabling innovation, which encourages startups104. Similarly, progress in entrepreneurship has mainly been driven by the private sector in Africa105. However, there is a need to take an integrative, cross-disciplinary and multi-sectoral approach to advance opportunities in the bioeconomy, including academia, industry, government, policymakers, where scientific knowledge can be leveraged not only for economic gains but for broader societal impact such as building pathways that empower the translation of research to market-ready solutions.

Summary of course content of selected practical workshops

The diversity of hands-on workshops (Fig. S1 and Table 1) conducted as part of the AfricaBP Open Institute regional workshops 2024 highlights the continent’s advancing capabilities in biodiversity genomics and bioinformatics (Box 2). Days 3–5 were focused on hands-on practicals to provide foundational exposures in genomics, bioinformatics, sample collections, ethics, and genome editing applicable to non-human species and hosted simultaneously across multiple sites during each scheduled regional workshop across all five African geographical regions. The AfricaBP brokered opportunities with 40 African institutions and industry partners to organize twenty-seven (27) hands-on practical workshops to introduce participants to cutting-edge technologies in genome sequencing, bioinformatics, sample collections, ethics, and genome editing, which trained 401 African researchers (see Table 1 for details, Fig. S1).

Table 1 Summary of course contents of selected practical workshops during the practical sessions of the AfricaBP Open Institute regional workshops 2024
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Several new hands-on practical workshop sites were added in 2024 and these include, but not limited to, IGH in Nigeria, Pwani University in Kenya, North-West University (NWU) and Stellenbosch University (SU) in South Africa, College of Computing at the University Mohammed VI Polytechnic (UM6P) in Morocco, and Higher Institute of Applied Biological Sciences of Tunis (ISSBAT) in Tunisia, while new hands-on practical workshop analysis types added in 2024 were simple sequence repeats (SSR) and transposable elements (TEs) in plants as well as genome editing using CRISPR/Cas9 technology (Table 1). For instance, Illumina’s hands-on practical workshops held at IGH, Nigeria, introduced participants to Illumina sequencing technology, in collaboration with their Africa-based partner, ISN Medical. This session focused on DNA extraction, PCR-free library preparations, sequencing and bioinformatics analysis of sequenced data, covering high-throughput sequencing platforms like the Illumina NextSeq 2000 and Illumina NovaSeq 6000 systems.

Similarly, the Oxford Nanopore Technology workshop, hosted at the University of Pretoria, South Africa, in collaboration with Distributed Platform in OMICS (DIPLOMICS), introduced participants to sequencing technologies with a focus on the PromethION flow cell system. Additionally, the MGI workshop, held at the Agricultural Research Council’s Biotechnology Platform, South Africa, demonstrated the full next-generation sequencing workflow using DNA Nanoballs Sequencing (DNBSEQ) technology, and finally, the Inqaba Biotec workshop in Nairobi, Kenya, provided participants with practical training in molecular biology and bioinformatics focused on DNA sequencing techniques, including DNA extraction from sponges and blood samples, PCR amplification, gel electrophoresis, and quality control assessment and sequencing data analysis.

The College of Computing at the University Mohammed VI Polytechnic (UM6P) in Morocco hosted a practical workshop on Simple Sequence Repeats and Transposable Elements in plants (Table 1), providing a comprehensive exploration of repetitive DNA sequences, their biological significance and the tools available for their identification and analysis. The workshop highlighted the importance of these tools for the progress of plant genome research. Additionally, the African Genome Center (AGC) at UM6P hosted a hands-on practical workshop, in partnership with Eppendorf and Thermo Fisher Scientific, which focused on genome editing using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) technology. CRISPR/Cas9 is one of the most revolutionary technologies in modern biology, enabling precise modifications of plant and animal genomes, with wide-ranging applications in research and agriculture106. The workshop also covered Basic Local Alignment Search Tool (BLAST) search and guide RNA (gRNA) design, both cloning-based and cloning-free editing techniques, and analysis of edited samples. In addition to the new themes, three new locations hosted practical workshops focused on genomic sequencing and bioinformatics, these include NWU and SU in South Africa and the ISSBAT in Tunisia. NWU’s practical workshop focused on Oxford Nanopore Technologies, covering library preparation, sequencing, and data analysis, SU’s Pathology Research Facility featured theoretical and practical sessions on metagenomic study design, DNA extraction and quality assessment, sequencing library preparation using the Oxford Nanopore MinION platform, and bioinformatics analysis while ISSBAT offered training on molecular biology techniques, metabarcoding, and microbial diversity analysis.

Fellowships and infrastructural development

In addition to the AfricaBP Open Institute’s efforts to empower African researchers and promote collaborations through annual regional workshops in 2024, the AfricaBP Open Institute also launched or awarded training fellowships through multi-stakeholder partnerships as well as defined roadmap for the African digital sequence information (DSI) databank containing information relating to biodiversity. Here, we discuss the training contents for these fellowships (see El Allali et al.107 for details of the African DSI databank roadmap107):

African Genome Center and AfricaBP Open Institute Joint Fellowship in Biodiversity Genomics and Bioinformatics

The AfricaBP Open Institute partnered with the African Genome Center (AGC) at the Mohammed VI Polytechnic University (UM6P) in Morocco to award an inaugural two-week residential and intensive hands-on Africa-based fellowship program for 10 African researchers3 in April 2024, which were selected from a pool of 545 applicants. The fellowship focused on the sequencing and analysis of the genome of Vachellia gummifera, a Moroccan endemic plant species of ecological and medical significance108. DNA extraction was followed by library preparation using the PCR-Free library kit to minimize biases typically associated with amplification-based methods109, and sequenced on the Illumina NextSeq 550 platform. The course content focused on building skills in high-throughput sequencing technologies, data quality control, and genome assembly. As a result, participants developed expertise in processing large genomic datasets and understanding species-specific genomic structures.

African biodiversity fellowship for emerging genomics leaders

The AfricaBP Open Institute partnered with Carl R. Woese Institute for Genomic Biology (IGB) at the University of Illinois Urbana-Champaign, United States3 to award an inaugural 3 months leadership fellowship to 4 African researchers from Morocco, Egypt, South Africa, and Nigeria, respectively, out of a total of 66 applications. The fellowship involves two phases: A one month Africa phase (May–September 2024) which was hosted by the AGC in Morocco, the International Center of Agriculture Research in Dry Areas (ICARDA) in Egypt, Inqaba Biotechnical Industries in South Africa, and MyAfroDNA in Nigeria, respectively, and a residential 3-month international phase (September–December 2024) which was hosted and funded by the IGB.

At the AGC, the training focused on genomic data analysis of Moroccan sheep and QTL mapping to identify regions associated with specific traits across different breeds. This bioinformatics-based program utilized R software for statistical computing110 for genetic diversity analysis and Python for QTL mapping through SheepQTLdb database111. The aim was to investigate the genetic basis of key traits, with potential applications in breeding programs and livestock management. At ICARDA, the training focused on the pipeline for Genome-Wide Association Studies for crop improvement using the GAPIT tool112 in R studio110 and programming and scripting using Python and Bash and handling file formats such as VCF113. At Inqaba Biotechnical Industries, the training focused on the Linux command line, bash scripting, and South Africa’s Center for High-Performance Computing (CHPC) platform’s PBS scheduler, job submission, job monitoring, job arrays, and environment modules, as well as theoretical and practical insights into PacBio Revio. At MyAfroDNA, the training focused on DNA extraction, polymerase chain reaction, and Sanger sequencing processes.

This international phase focused on providing research exposure and advanced skill development, equipping African fellows with team science techniques applicable to genomics leadership in biodiversity research. At the IGB, each fellow was posted to one of the 15 multi-investigator, multidisciplinary Research Themes: Center for Genomic Diagnostics, Genomic Ecology of Global Change, and Biosystems Design, respectively.

Within the Center for Genomic Diagnostics, fellows: (a) explored the use of nanomaterials for targeted drug delivery, imaging, and therapeutic applications, novel drug delivery systems, such as nanocarriers and smart materials, that can more efficiently deliver cancer therapies while reducing side effects, (b) executed a project on the use of advanced diagnostic tools and biosensors for disease detection and monitoring, (c) performed analysis using scanning electron microscopy for the examination of material compositions and surface structures at the microscale, transmission electron microscopy for the high-resolution characterization of the size, shape, and morphology of nanomaterials, and Immunofluorescence and the theory, use, and interpretation of enzyme-linked immunosorbent assay data, (d) introduced to mammalian cell culture, flow cytometry, confocal microscopy, fluorescence microscopy, and cell viability tests such as MTT assays to identify the best materials for targeted drug administration, and (e) examined the hotspot point mutations in acute myeloid leukemia (AML) utilizing the computational biology expertise and knowledge they acquired during the program’s African phase.

Within the Genomic Ecology of Global Change Theme, one of the fellows was assigned to the photosynthesis engineering laboratory, which focuses on enhancing photosynthesis in crops and algae by studying molecular mechanisms and identifying components that reveal plant responses to external and internal cues. The fellow carried out a project on the dual nature of plant genome promoters, tested their expression levels in plants, and bioinformatically identified native bidirectional promoters114, which are 1000 bp intergenic regions between head-to-head gene pairs. This research was performed in the model plant Arabidopsis thaliana using R scripting and bash programming. Candidate bidirectional pairs were filtered based on the proximity between gene pairs and their correlation to identify potential bidirectional promoters. After filtration, gene pairs were categorized into positive correlation (genes that tend to increase expression and together) and negative correlation (genes that tend to decrease expression together)115 while the bidirectional promoters assigned to the positively correlated genes were programmed for further screening via transient transformation into other model plants.

Finally, one of the fellows was assigned to The Biosystems Design Theme, which focuses on developing and applying synthetic biology, machine learning, and laboratory automation tools to address society’s most daunting challenges in human health and energy and investigating the fundamental aspects of enzyme catalysis, cell metabolism, and gene regulation116. The fellow’s project focused on developing a new-to-nature hydroaminoalkylation reaction for the synthesis of chiral amines, which serve as useful building blocks to pharmaceuticals, agrochemicals, and specialty chemicals by synergizing photocatalysis and biocatalysis and by using directed evolution. Some of the techniques employed in the course of the project include protein engineering, high-performance liquid chromatography, and identification of biosynthetic gene clusters (BGCs) using resources such as antiSMASH117.

African plant genome assembly and annotation fellowship

The AfricaBP Open Institute partnered with the International Institute of Tropical Agriculture (IITA), Nigeria, and Inqaba Biotec, West Africa, to launch the inaugural edition of the African plant genome assembly and annotation fellowship in June 2024, which will feature a hybrid format fellowship combining an 8-week virtual phase starting in Q1 2025 and a 10-day on-site intensive training at the IITA headquarters in Ibadan, Nigeria, scheduled for April 2025. A total of 10 fellows have been selected from 261 applicants, with notifications scheduled for first quarter of 2025. The virtual phase is designed to equip participants with advanced knowledge in genome biology, PacBio HiFi and Omni-C sequence reads, methods for data quality control, assembling and assessing long- and short-reads, and estimating genome assembly completeness. It will also include training in gene prediction and functional annotation techniques, including annotating gene sets with associated functional information.

Conclusion, recommendations, and future directions

The AfricaBP Open Institute is making intentional progress in addressing AfricaBP’s Grand Challenges, focusing, in 2024, on using biodiversity genomics and bioinformatics to support Africa’s bioeconomy. By combining advanced technologies with local strategies, AfricaBP has expanded its understanding of bioeconomy frameworks and identified sustainable pathways to address Africa’s biodiversity challenges. One key effort is providing a platform for national networks of scientists to expand local sequencing infrastructures and capabilities. The proposed 1000 Moroccan Genome Project case study demonstrates how investments in genomics can deliver significant returns, with a 3.29 Benefit–Cost ratio and $28 million net present value over10 years. Establishing local sequencing hubs will reduce foreign dependency, create skilled jobs, lower costs, and accelerate innovation, strengthening Africa’s competitiveness in the global genomics landscape. Equally important is the focus on high-impact agricultural applications. Prioritizing the development of drought-resistant crops and disease-resilient livestock could address over 53% of Africa’s projected economic output tied to agriculture, while also enhancing food security and positioning African nations as leaders in sustainable agricultural innovation.

Capacity building and strengthening remains a central pillar of AfricaBP’s strategy. Through specialized curricula, research programs, and inter-Africa and inter-continental collaborations, the AfricaBP Open Institute is cultivating a skilled genomics and bioinformatics workforce capable of driving innovation in agriculture and biodiversity conservation. Strengthened public–private partnerships, supported by fiscal incentives, streamlined regulations, and transparent frameworks, will attract investment, accelerate technology transfer, and stimulate market growth for genomics-based products. Additionally, AfricaBP’s roadmap for a transformative digital sequence information (DSI) database marks a critical step forward. Directing sequencing efforts toward high-priority species in biodiversity-rich areas will protect Africa’s genetic resources, enhance climate resilience, and support ecosystems critical to sustainable economic gains. To ensure lasting impact, AfricaBP is advocating for robust data policies aligned with national genetics resources and digital sequence information framework98,107. These policies aim to safeguard genomic information, preserve indigenous knowledge, and ensure equitable benefit-sharing, creating a foundation that aligns genomics research with broader regional priorities and further accelerates Africa’s collective bioeconomy potential.