African scientists are launching a revolution in biodiversity genomics

Although Africa is home to the second largest collection of biodiversity on earth, many of its unique plants, animals and microbes are threatened with extinction due to human activity and climate change.

Tragically, very little is known about many of these species – a lack of knowledge that deprives the world of innovation and solutions to pressing challenges in food, nutrition and health.

But that is about to change. A group of African scientists – experts in genetics, genomics and bioinformatics – have set themselves the ambitious goal of uncovering the secrets of plant and animal diversity across the continent through a unique genome sequencing project.

Rich variety, limited knowledge

Launched in 2021, the African BioGenome Project (AfricaBP) seeks to sequence the genomes of 105,000 endemic plants, animals, fungi and other organisms of economic, scientific and cultural importance.

The project, which currently involves more than 109 African scientists and 22 African organizations, will decode each organism to study the rich biodiversity of 2,500 native African species, including Boyle’s beaked blind snake (Rhinotyphlops boylei) from South Africa and red mangroveRhizophora mangla) from Nigeria.

Genome consistency will inform biodiversity conservation across Africa and strengthen the continent’s ability to meet the goals of the post-2020 Global Diversity Framework Convention on Biodiversity (CBD), said Apolitaner Jickeng, a genomics scientist and director of the Center for Biodiversity. genetics of tropical animals. and Health at the Roslin Institute at the University of Edinburgh. He is one of the promoters of AfricaBP.

The need to understand Africa’s rich biodiversity is long overdue, says ThankGod Ebenezer, a bioinformatics specialist at the European Institute of Bioinformatics (EMBL-EBI) in the United Kingdom who participates in AfricaBP. To date, sequencing by Africans in Africa is insignificant, he said.

Africa can build capacity and expertise in genome sequence analysis, as demonstrated by projects such as the African Heredity and Health Consortium (H3Africa), Ebenezer said. However, Africa lags behind in the sequence of its native species for the benefit of its people.

The genome is the heart of every living organism, containing the codes that dictate its appearance and much of its behavior, for example. Sequencing allows the decoding of any organism to study biodiversity.

“The main driver here is the rich biodiversity we have in Africa, both in the plant community and in animal communities, as well as microbes,” Jikeng said.

Biodiversity hotspots

Africa is home to eight of the world’s biodiversity hotspots and tropical forests in the Congo Basin, which alone account for 10 percent of the world’s biodiversity. Biodiversity hotspots are areas identified as the most biologically rich in the world, according to the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES).

Prof. Apollinaire Jickeng, Director of the Center for Tropical Animal Genetics and Health at the University of Edinburgh. Photo: Maverick Photo Agency

Climate change will exacerbate the effects of past threats to biodiversity, with Africa being one of the regions most likely to be affected, according to the latest report from the Intergovernmental Panel on Climate Change (IPCC).

The project is driven by the urgency of expanding access and sharing the benefits of biological resources across Africa, Ebenezer said. Various international agencies and agreements share this goal.

The United Nations Nagoya Protocol on Access and Benefit-sharing advocates fair and equitable sharing of genetic resources, while the new Global Framework for Nature Management by 2030 identifies the conservation of wildlife and the conservation of at least 90 percentage of their genetic diversity as one of the 10 main stages.

Jikeng described the Africa Biogen Project as a long-term ambitious vision for Africa to complete genome sequencing of various species.

“It will not happen today or tomorrow. “It’s a long-term vision, but we hope to build a genomic education in Africa along the way to appreciate the importance of this discipline,” Jikeng said.

The project will use genomic information to diagnose and accelerate plant and animal breeding, in addition to building an infrastructure and ecosystem for genomic science in Africa, to benefit local communities that preserve the unique species, he added.

Catch-up game

Around 3,000 animal and 800 plant genomes have been sequenced worldwide. And yet only 20 of the plants are African species, although there are 45,000 plant species on the continent, second only to South America. None of the 20 have been sequenced in Africa, Ebenezer said. Similarly, only 300 of the animals are from Africa and only 11 are sequenced on the continent.

“We are not where we should be,” said Jicken, who has sequenced many genomes, including that of a pathogen that causes sleeping sickness in humans and animals.

“Past genome projects have looked at plant species that are native to Africa, but this sequencing has been done in the United States or Europe,” Jickeng said. “We have some sequencing platforms and laboratories on the African continent, but we have not built what is next to analyze the data in Africa. In order to ask and answer other scientific questions in Africa, we are still relying heavily on Europe, North America and elsewhere to realize our ambition for genomics.

“We missed it, but the latest examples show that we can catch up. “If you look at COVID and Ebola, many well-established genomic scientists in Africa have saved the day,” Jickeng said, citing the work of Prof. Tulio de Oliveira in South Africa, Dr. Samuel Oyola in Kenya and Prof. Christian Happi in Nigeria. About 70 percent of Africa’s genomic sequencing capacity is concentrated in South Africa, Kenya, Nigeria, Morocco and Egypt.

A billion dollar vision

AfricaBP will be implemented for a decade, and researchers estimate it will require funding of about $ 100 million a year. It will bring together 55 African researchers and politicians from genomics, bioinformatics, biodiversity and agriculture – 11 for each of the geographical regions of the African Union, according to a document published in Nature in March 2022.

$ 1 billion will come from governments, industry and bilateral financiers, Jikeng explained. African universities, which are already involved in genomic science, are interested in the project.

The African Union is also excited about the project, Jikeng said. The AU sees the project implementing its 2063 program, which recognizes science, technology and innovation as key drivers and tools for achieving the development goals of the AU and the Member States.

To further support the project, the AfricaBP Open Institute for Genomics and Bioinformatics was established as a platform for knowledge sharing for capacity building, training and for industry people who want to connect with genomics experts across Africa. The transfer of materials is a key political issue, Ebenezer said.

Image: The flower of the African spider (Cleome Gynandra) is one of the endemic plant species whose genome will be sequenced. Photo: Busani Bafana


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