Chromosome-scale assembly of the African yam bean genome
Abstract 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 incl...
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Nature Portfolio
2024-12-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-024-04210-2 |
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| author | Bernice Waweru Isaac Njaci Rajneesh Paliwal Mary Maranga Collins Muli Edwin Murungi Davies Kaimenyi Beatus Lyimo Helen Nigussie Bwihangane Birindwa Ahadi Ermias Assefa Hassan Ishag Oluwaseyi Olomitutu Michael Abberton Christopher Darby Cristobal Uauy Nasser Yao Daniel Adewale Peter Emmrich Jean-Baka Domelevo Entfellner Oluwaseyi Shorinola |
| author_facet | Bernice Waweru Isaac Njaci Rajneesh Paliwal Mary Maranga Collins Muli Edwin Murungi Davies Kaimenyi Beatus Lyimo Helen Nigussie Bwihangane Birindwa Ahadi Ermias Assefa Hassan Ishag Oluwaseyi Olomitutu Michael Abberton Christopher Darby Cristobal Uauy Nasser Yao Daniel Adewale Peter Emmrich Jean-Baka Domelevo Entfellner Oluwaseyi Shorinola |
| author_sort | Bernice Waweru |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-67be2c946fb747a38151eb849254e80a |
| institution | OA Journals |
| issn | 2052-4463 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-67be2c946fb747a38151eb849254e80a2025-08-20T01:59:48ZengNature PortfolioScientific Data2052-44632024-12-0111111110.1038/s41597-024-04210-2Chromosome-scale assembly of the African yam bean genomeBernice Waweru0Isaac Njaci1Rajneesh Paliwal2Mary Maranga3Collins Muli4Edwin Murungi5Davies Kaimenyi6Beatus Lyimo7Helen Nigussie8Bwihangane Birindwa Ahadi9Ermias Assefa10Hassan Ishag11Oluwaseyi Olomitutu12Michael Abberton13Christopher Darby14Cristobal Uauy15Nasser Yao16Daniel Adewale17Peter Emmrich18Jean-Baka Domelevo Entfellner19Oluwaseyi Shorinola20International Livestock Research Institute, P.O. Box 30709International Livestock Research Institute, P.O. Box 30709Genetic Resources Center, International Institute of Tropical Agriculture, Oyo RoadDepartment of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000International Livestock Research Institute, P.O. Box 30709Department of Medical Biochemistry, Kisii University, P.O. Box 408-40200Bioscience Research Centre (PUBReC), Pwani University, P.O Box 195-80108Nelson Mandela African Institute of Science and TechnologyDepartment of Microbial Cellular and Molecular Biology, Addis Ababa UniversityUniversité Evangélique en Afrique, UEA, Faculty of Agriculture and Environment sciencesDepartment of Agronomy, Horticulture and Plant Science, South Dakota State UniversityCollege of Veterinary Sciences, University of NyalaGenetic Resources Center, International Institute of Tropical Agriculture, Oyo RoadGenetic Resources Center, International Institute of Tropical Agriculture, Oyo RoadJohn Innes Centre, Norwich Research ParkJohn Innes Centre, Norwich Research ParkBiosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, International Livestock Research InstituteDepartment of Crop Science and Horticulture, Federal University Oye-EkitiJohn Innes Centre, Norwich Research ParkInternational Livestock Research Institute, P.O. Box 30709International Livestock Research Institute, P.O. Box 30709Abstract 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.https://doi.org/10.1038/s41597-024-04210-2 |
| spellingShingle | Bernice Waweru Isaac Njaci Rajneesh Paliwal Mary Maranga Collins Muli Edwin Murungi Davies Kaimenyi Beatus Lyimo Helen Nigussie Bwihangane Birindwa Ahadi Ermias Assefa Hassan Ishag Oluwaseyi Olomitutu Michael Abberton Christopher Darby Cristobal Uauy Nasser Yao Daniel Adewale Peter Emmrich Jean-Baka Domelevo Entfellner Oluwaseyi Shorinola Chromosome-scale assembly of the African yam bean genome Scientific Data |
| title | Chromosome-scale assembly of the African yam bean genome |
| title_full | Chromosome-scale assembly of the African yam bean genome |
| title_fullStr | Chromosome-scale assembly of the African yam bean genome |
| title_full_unstemmed | Chromosome-scale assembly of the African yam bean genome |
| title_short | Chromosome-scale assembly of the African yam bean genome |
| title_sort | chromosome scale assembly of the african yam bean genome |
| url | https://doi.org/10.1038/s41597-024-04210-2 |
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