Chromosome-scale assembly of the African yam bean genome
Genomics-informed breeding of locally adapted, nutritious, albeit underutilised African crops can help mitigate food and nutrition insecurity challenges in Africa, particularly against the backdrop of climate change. However, utilisation of modern genome-assisted crop improvement tools including genomic selection and genome editing for many African indigenous crops is hampered by the scarcity of genomic resources. Here we report on the assembly of the genome of African yam bean (Sphenostylis stenocarpa), a tuberous legume crop that is indigenous to Africa. By combining Nanopore-based assembly with Hi-C scaffolding, we produced a high-quality chromosome-scale assembly with an N50 of 69.5 Mbp. Using transcriptome evidence from Nanopore RNASeq and protein homology evidence from related crops, we predicted and annotated 31,614 putative protein coding genes. We also show how this genome substantially improves anchoring of genetic markers from African yam bean, confirming its significance as a resource for genetic research in African yam bean.
Authors
- Michael Abberton (ORCID: https://orcid.org/0000-0003-2555-9591)
- Oluwaseyi E. Olomitutu (ORCID: https://orcid.org/0000-0002-3628-7707)
- Christopher Darby
- Oluwaseyi Shorinola (ORCID: https://orcid.org/0000-0003-3516-303X)
- Jean-Baka Domelevo Entfellner (ORCID: https://orcid.org/0000-0002-8282-1325)
- Bernice Waweru (ORCID: https://orcid.org/0000-0002-1788-1567)
- Helen Nigussie (ORCID: https://orcid.org/0000-0001-8261-1718)
- Nasser Yao (ORCID: https://orcid.org/0000-0002-1183-708X)
- Beatus Lyimo (ORCID: https://orcid.org/0000-0002-6743-4546)
- Peter M. F. Emmrich (ORCID: https://orcid.org/0000-0001-5085-9575)
- Ahadi Bwihangane Birindwa (ORCID: https://orcid.org/0000-0003-4891-5528)
- Daniel B. Adewale (ORCID: https://orcid.org/0000-0002-0249-8629)
- Mary Maranga (ORCID: https://orcid.org/0000-0003-3496-8776)
- Isaac Njaci (ORCID: https://orcid.org/0000-0001-9649-6650)
- Collins Muli (ORCID: https://orcid.org/0000-0003-1775-0468)
- Davies Kaimenyi (ORCID: https://orcid.org/0000-0002-6320-3740)
- Cristóbal Uauy (ORCID: https://orcid.org/0000-0002-9814-1770)
- Rajneesh Paliwal (ORCID: https://orcid.org/0000-0001-6493-3289)
- Edwin Murungi (ORCID: https://orcid.org/0000-0001-9896-0664)
- Hassan Zackaria Ali Ishag (ORCID: https://orcid.org/0000-0003-4723-1909)
- Ermias Assefa
Institutions
- John Innes Centre (GB)
- University of East Anglia (GB)
- Jagiellonian University (PL)
- The University of Queensland (AU)
- South Dakota State University (US)
- Jomo Kenyatta University of Agriculture and Technology (KE)
- Pwani University (KE)
- Norwich Research Park (GB)
- Université Officielle de Bukavu (CD)
- Université Evangélique en Afrique (CD)
- University of Nyala (SD)
- Agriculture and Food (AU)
- Kisii University (KE)
- Hochschule Geisenheim University (DE)
- Federal University Oye Ekiti (NG)
- Addis Ababa University (ET)
- International Livestock Research Institute (KE)
- International Institute of Tropical Agriculture (NG)
- University of Birmingham (GB)
- Nelson Mandela African Institution of Science and Technology (TZ)
Publication Details
- Journal
- Scientific Data
- Published
- 2024-12-18
- DOI
- https://doi.org/10.1038/s41597-024-04210-2
- Citations
- 4
- Primary Topic
- Legume Nitrogen Fixing Symbiosis
- Type
- article
- Field-Weighted Citation Impact
- 2.40
Funders
- American Breast Cancer Foundation
- Royal Society
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council