Chromosome-scale assembly of the African yam bean genome
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Date
2023-11-01
Journal Title
Journal ISSN
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Publisher
Cold Spring Harbor Laboratory
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
crop improvement tools including genomic selection and genome editing for many
African indigenous crops is hampered by the scarcity of genetic and 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 long and short read sequencing with Hi-C scaffolding, we produced a
chromosome-scale assembly with an N50 of 69.5 Mbp and totalling 649 Mbp in
length (77 - 81% of the estimated genome size based on flow cytometry). Using
transcriptome evidence from Nanopore RNA-Seq and homology evidence from
related crops, we annotated 31,614 putative protein coding genes. We further show
how this resource improves anchoring of markers, genome-wide association analysis
and candidate gene analyses in Africa yam bean. This genome assembly provides a
valuable resource for genetic research in Africa yam bean.
Sustainable Development Goals
A research article was published by bioRxiv preprint, 2023
Keywords
Research Subject Categories::NATURAL SCIENCES