Sequencing in Africa: Lessons learned from building chromosome-level plant genomes

As Africa advances toward sequencing and understanding its vast biodiversity, locally led genomics projects are helping to shape a new model for research, innovation, and equity on the continent. A recent initiative led by the South African Medical Research Council (SAMRC) Genomics Platform, in partnership with DIPLOMICS, the 1,000 South African Genomes (1KSA) initiative, African BioGenome Project (AfricaBP), and MGI Tech, set out to generate the first chromosome-level plant genome assemblies conducted entirely in Africa using Oxford Nanopore Technology and Hi-C. The experience revealed both the enormous potential of Africa-based genomics and the practical and ethical challenges that must be navigated along the way.

One of the first lessons learned involved the technical complexity of obtaining high-quality nucleic acids from hardy plant material. Unlike animal or microbial systems, plants often contain high levels of secondary metabolites and polysaccharides that can interfere with downstream sequencing. Developing optimized, reproducible extraction protocols suitable for long-read sequencing required extensive troubleshooting and training. Although time-consuming, this process ultimately strengthened local expertise, laboratory workflows, and standard operating procedures that will benefit future African genomics projects.

A second major challenge involved the onboarding of new sequencing and scaffolding technologies, particularly Hi-C, which can be used to map the three-dimensional organisation of a genome within a cell. While Hi-C offers powerful chromosomal resolution, its application demands specialized technical and analytical skills. The team worked closely with MGI Tech and consulted global partners, including members of the AfricaBP network, to refine laboratory workflows, sequencing strategies, and data interpretation pipelines. Through these collaborations, local researchers gained hands-on experience in applying state-of-the-art techniques, laying a foundation for sustainable, in-continent genomic research.

The analytical stage introduced its own learning curve. With hundreds of available tools for genome assembly, polishing, and annotation, identifying the most appropriate combination for complex plant genomes was far from straightforward. Selecting tools such as Hifiasm for assembly, integrating RNA sequencing data, and ensuring accuracy through manual curation required extensive benchmarking and guidance from the AfricaBP network. These efforts reinforced the importance of knowledge exchange and collaborative problem-solving, both within and beyond Africa — demonstrating how open communication accelerates capacity building and scientific discovery.

Beyond the technical aspects, the project also prompted deeper reflection on ethics, data governance, and genomic data sharing. While open data is central to scientific transparency and progress, it carries particular risks for Africa, where unique biodiversity holds immense ecological, traditional, scientific, and economic value. The team coped with the challenge of ensuring that genomic data are “as open as possible, but as closed as necessary”: accessible for academic research, yet protected from potential exploitation or unacknowledged commercial use. Developing fair, context-sensitive data sharing frameworks is currently ongoing discussion within AfricaBP and related initiatives. The AfricaBP has recently published Practical Guide To Accessing And Sharing Biological Diversity Material And Data - A Research Stage-Based Approach (https://osf.io/83dxn/files/5zthf), published a preprint on African genomics in the era of the Global Biodiversity Framework (https://doi.org/10.31219/osf.io/2xq5e), as well as launched the 1st African Congress on Digital Sequence Information, Infrastructure Development and Policy (African Congress on DSI) (https://www.linkedin.com/posts/african-biogenome-project_we-are-launching-1st-african-congress-on-activity-7383856047234600960-O5QK/) to further guide African researchers on ethics, data governance, and sharing of genetic materials and genomics data and power African DSI infrastructures through deeper policy discourse.

Despite these challenges, the outcomes have been transformative. The experience demonstrated that with access to modern infrastructure, institutional support, and collaborative networks, high-quality, chromosome-level genome assemblies can be produced entirely within Africa. Each obstacle encountered, whether technical, analytical, or ethical, became an opportunity for skill development and reflection. Importantly, the lessons learned extend beyond a single species or project, informing best practices for future biodiversity genomics efforts across the continent.

As AfricaBP continues to promote genomics for conservation, sustainable use, and equitable innovation, projects like this one illustrate both the promise and complexity of achieving that vision. Building genomic capacity in Africa requires more than sequencing technologies, it demands long-term investment in people, infrastructure, ethics, and collaboration. The journey toward a truly African-led genomics ecosystem is ongoing, but with each project, the continent moves closer to defining its own path in global biodiversity research.

Author information:
Dr Ansia van Coller

South African Medical Research Council (SAMRC) Genomics Platform

https://www.samrc.ac.za/research/centre-and-platforms-office/genomics-meet-our-team 

Short Biography: Dr Ansia van Coller is a Senior Scientist at the SAMRC Genomics Platform in South Africa, where she applies bioinformatics and genome assembly approaches to study biodiversity and health. She leads pioneering plant genomics projects and is passionate about building African capacity in genome research through initiatives such as the African BioGenome Project and the 1,000 South African Genomes (1KSA) initiative.