Chromosome-scale genome assembly of Vigna radiata IPM-02-03. An improved chromosome-scale genome assembly of Indian Vigna radiata cultivar enables delineation of centromere and telomere in the crop

Vigna radiata (L.) R. Wilczek var. radiata (mungbean) is a widely consumed pulse crop holding significant economic importance ensuring both the global protein security and sustainable crop production. While three reference assemblies are available for the crop, the chromosomal features including centromeric and telomeric regions have remained unresolved. Additionally, a high-quality reference genome originating from the crop's centre of origin is still pending which can uncover novel genetic variation for agriculture implementation. In this study, we present a chromosome-level reference genome of V. radiata Indian cultivar, IPM-02-03 achieved through a combination of long-read PacBio HiFi sequencing and high throughput chromatin capture Hi-C sequencing. The assembled genome spans a total length of ~596 Mb equating to ~98% of the predicted genome size and features a N50 value of 10.35Mb. Around 502 Mb of the assembled genome is anchored on 11 pseudochromosomes conforming to the chromosome count in the crop. Telomeres and centromeres are distinctly identified in this study, elucidating essential genomic features. Over 56.38 % of the assembly is spanned by repeat elements. The BUSCO analysis indicated a gene completeness score of 98.5%. Similarly, the LAI score index demonstrated a completeness score of 16.58. Present assembly was able to close many gaps in the previous reference assemblies and provides a high quality assembly from a cultivar (IPM-02-3) which is known for its robust resistance against mungbean yellow mosaic virus (MYMV). A more complete genome will provide a reliable standard genome which will help in significantly accelerating mungbean breeding programs.