Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China.

Munage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is renowned for its exceptional fruit traits. There are two main types of Munage: white fruit (WM) and red fruit (RM). However, the lack of a high-quality genomic resources has impeded effective breeding and restricted the potential for expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies for WM and RM, alongside integrated whole genome resequencing (WGS) data and transcriptome data to illuminate the origin, private mutations and selection in Munage. Our analyses suggest that Munage likely shares a common ancestor with Eurasian grapes that originated in West Asia. Selective analysis between Munage clones and Eurasian grapes mapped genomic signals of selection in Munage grapes, with genes enriched in processes including cell maturation, plant epidermal cell differentiation, and root epidermal cell differentiation. We also identified 283 somatic mutation sites between WM and RM, along with differential selection on genome and expressed genes. These findings provide crucial genetic resources for investigating the genetics of the ancient Chinese grape variety, Munage, and will facilitate the genetic improvement in grapevine using this ancient cultivar as a gene donor.