High-contiguity genome assembly of moth bean (Vigna aconitifolia) reveals genes for disease resistance and flavonoid biosynthesis

Abstract

Moth bean (Vigna aconitifolia), a protein-rich, arid-adapted legume of considerable agronomic importance, lacks a whole genome assembly, limiting genome-enabled trait discovery and genetic improvement. In this study, we estimated its genome size using 31.28 Gb of Illumina short-read sequencing data, and a k-mer analysis (k = 21) predicted a genome size of 448.98 Mb. We generated a highly contiguous 420.3 Mb genome assembly using 37.04 Gb of PacBio HiFi long-read sequencing data, corresponding to 82.5× genome coverage. The assembly achieved a contig N50 of 22.30 Mb, with a maximum contig length of 59.6 Mb, and exhibited >98% completeness based on BUSCO assessment. Comparative genomic and phylogenetic analyses of 14 closely related species identified V. radiata and V. mungo as the closest extant relatives of moth bean, with an estimated divergence time of ~3.7 Mya, consistent with established phylogenetic relationships within the genus Vigna. Structural annotation predicted ~27,434 protein-coding genes, of which 27,411 (99.91%) were functionally annotated. Repetitive sequences accounted for 50.66% of the genome, with retrotransposons representing the predominant class and occupying 109.9 Mb (26.1%). We further identified 178 disease resistance–related genes and 54 genes involved in flavonoid biosynthesis, including those encoding key enzymes such as chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, and flavone synthase II. Collectively, we present the first highly contiguous moth bean genome assembly, providing a foundational resource for evolutionary, functional genomics and breeding studies. This resource facilitates characterization of genes governing disease resistance and flavonoid biosynthesis, supporting genetic improvement of stress tolerance and nutritional quality in moth bean.