Data from: The jujube genome provides insights into genome evolution and the domestication of sweetness/acidity taste in fruit trees

Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to the recent insertions of transposable elements in the 'Dongzao' genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication.

枣（Ziziphus jujuba Mill.）隶属于鼠李科（Rhamnaceae），是一种兼具极高经济价值与营养价值的广受欢迎的果树树种。本研究报道了干枣品种‘晋枣（Junzao）’的基因组草图，并对31份地理来源多样的栽培枣与酸枣（Ziziphus jujuba var. spinosa）种质开展了基因组重测序。比较基因组分析显示，鲜食枣品种‘冬枣’的基因组较‘晋枣’大约86.5 Mb，该差异部分源于‘冬枣’基因组中近期发生的转座元件插入事件。本研究构建了蔷薇目（Rosales）下两个姊妹科——鼠李科与蔷薇科（Rosaceae）的共同祖先的8条原始染色体，阐明了塑造现代枣基因组结构的演化过程。群体结构分析揭示，枣与其野生近缘种间广泛的杂交事件造就了枣复杂的遗传背景。值得注意的是，研究在选择扫荡区域中鉴定出多个调控果实有机酸代谢与糖分含量的关键基因。本研究还鉴定了控制配子体自交不亲和性的S位点基因，并分析了枣基因组中S位点的单倍型模式。本研究为枣的遗传改良提供了宝贵的基因组资源，同时为枣的基因组演化、群体结构及驯化过程提供了新的见解。