Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication
Mingxin Guo, Qun Lian, Ye Wen Mei, Wangwang Yang, Shun-Ge Zhao, Siyuan Zhang, Xue Xing, H.-B. Zhang, K L Gao, Wenjie He, Zhitong Wang, Huan Wang, Jun Zhou, Lin Cheng, Zhigui Bao, Sanwen Huang, Jianbin Yan, Xusheng Zhao
Abstract
Jujube (Ziziphus jujuba Mill.), belonging to the Rhamnaceae family, is gaining increasing prominence as a perennial fruit crop with significant economic and medicinal values. Here, we conduct de novo assembly of four reference-grade genomes, encompassing one wild and three cultivated jujube accessions. We present insights into the population structure, genetic diversity, and genomic variations within a diverse collection of 1059 jujube accessions. Analyzes of the jujube pan-genome, based on our four assemblies and four previously released genomes, reveal extensive genomic variations within domestication-associated regions, potentially leading to the discovery of a candidate gene that regulates flowering and fruit ripening. By leveraging the pan-genome and a large-scale resequencing population, we identify two candidate genes involved in domestication traits, including the seed-setting rate, the bearing-shoot length and the leaf size in jujube. These genomic resources will accelerate evolutionary and functional genomics studies of jujube. Jujube is a perennial fruit crop with significant economic and medicinal values. Here, the author report genome assemblies of four jujube accessions, construct pan-genome together with four previously published genomes, and generate resequencing data to reveal genetic basis of domestication traits.