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 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.