Chromosome-scale assembly of the African yam bean genome

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

doi:10.1038/s41597-024-04210-2

Chromosome-scale assembly of the African yam bean genome

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^*

^*Corresponding author for this work

Biosciences

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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.

Original language	English
Article number	1384
Number of pages	11
Journal	Scientific Data
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41597-024-04210-2
Publication status	Published - 18 Dec 2024

Bibliographical note

Copyright:
© The Author(s) 2024.

ASJC Scopus subject areas

Statistics and Probability
Information Systems
Education
Computer Science Applications
Statistics, Probability and Uncertainty
Library and Information Sciences

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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WaweruB2024ChromosomeFinal published version, 2.55 MBLicence: Creative Commons: Attribution (CC BY)

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Waweru, B., Njaci, I., Paliwal, R., Maranga, M., Muli, C., Murungi, E., Kaimenyi, D., Lyimo, B., Nigussie, H., Ahadi, B. B., Assefa, E., Ishag, H., Olomitutu, O., Abberton, M., Darby, C., Uauy, C., Yao, N., Adewale, D., Emmrich, P., ... Shorinola, O. (2024). Chromosome-scale assembly of the African yam bean genome. Scientific Data, 11(1), Article 1384. https://doi.org/10.1038/s41597-024-04210-2

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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.",

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Waweru, B, Njaci, I, Paliwal, R, Maranga, M, Muli, C, Murungi, E, Kaimenyi, D, Lyimo, B, Nigussie, H, Ahadi, BB, Assefa, E, Ishag, H, Olomitutu, O, Abberton, M, Darby, C, Uauy, C, Yao, N, Adewale, D, Emmrich, P, Entfellner, JBD & Shorinola, O 2024, 'Chromosome-scale assembly of the African yam bean genome', Scientific Data, vol. 11, no. 1, 1384. https://doi.org/10.1038/s41597-024-04210-2

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AU - Murungi, Edwin

AU - Kaimenyi, Davies

AU - Lyimo, Beatus

AU - Nigussie, Helen

AU - Ahadi, Bwihangane Birindwa

AU - Assefa, Ermias

AU - Ishag, Hassan

AU - Olomitutu, Oluwaseyi

AU - Abberton, Michael

AU - Darby, Christopher

AU - Uauy, Cristobal

AU - Yao, Nasser

AU - Adewale, Daniel

AU - Emmrich, Peter

AU - Entfellner, Jean Baka Domelevo

AU - Shorinola, Oluwaseyi

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Chromosome-scale assembly of the African yam bean genome

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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