Ziziphus jujuba cultivar:Dongzao Genome sequencing. Ziziphus jujuba cultivar:Dongzao

This study provides the first gapless genome assembly of jujube (Ziziphus jujuba Mill.), an increasingly popular fruit tree worldwide for its nutritional and medicinal benefits as well as outstanding drought and saline-alkali tolerance. The 12 chromosomes, measured 393,332,932 bp in size with 29,633 protein-coding genes, were each assembled into a single gapless contig, representing the best assembly quality in the Rhamnaceae family. Approximately 57.06% of the genome were repetitive sequences, including all recognized telomeres and putative centromeres. Duplication analysis based on the paralogs revealed an undetected small scale of recent duplication which might representing an ongoing species-specific duplication in jujube. Speciation analysis based on the orthologs indicated that cultivated and wild jujube typically belong to the same species. Spatial chromatin architecture analysis revealed that larger sizes of the topologically associating domains (TADs) containing fewer genes per unit length. The largest TAD (1.55 Mb) is composed of the transferred chloroplast sequences, which provides new clues to study the way of organizing the chloroplast fragments transferred to the nucleus in plants. A total of 13 jujube-specific monodehydroascorbate reductase (MDAHR) genes, which is vital in the vitamin C recycling pathway, were identified to tandemly packed in a 163 kb region of chromosome 1 with frequent intra-interactions, which would serve as an important information for further research on vitamin C accumulation in jujube.