Chinese jujube (Ziziphus jujuba Mill.) is one of the most important deciduous tree fruits in China, with substantial economic and nutritional value. Jujube was domesticated from its wild progenitor, wild jujube (Z. jujuba var. spinosa), with high medicinal value. Here, we report the 767.81Mb and 759.24 Mb haplotype-resolved assembly of a dry-eating ‘Junzao’ jujube (JZ) and a wild jujube accession (SZ), using a combination of multiple sequencing strategies. Each assembly yielded two complete haplotype-resolved genomes at the telomere-to-telomere (T2T) level, and about 81.60Mb and 69.07Mb of structural variation (SV) were found between the two haplotypes within JZ and SZ, respectively. Comparative genomic analysis revealed a large inversion on each chromosome 3 and 4 between JZ and SZ, and numerous genes were affected by SVs, some of which were associated with starch and sucrose metabolism. A large-scale population analysis of 672 accessions revealed that wild jujube originated from the lower reaches of Yellow River and initially domesticated at the local sites, meanwhile, it was spread widely and then independently domesticated at the Shanxi-Shaanxi Gorge of the middle Yellow River. In addition, we identified some new selection signals on genomes, such as tissue developments, pollination, associated with jujube domestication on tree size, fertilization and etc. In conclusion, our study provides high-quality reference genomes of jujube and wild jujube and new insights into the domestication history of jujube.

中文翻译：

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Ziziphus jujuba 和 Z. jujuba var. 的两个单倍型解析的 T2T 参考基因组。刺糖为枣驯化提供新见解

枣（Ziziphus jujuba Mill.）是我国最重要的落叶树果之一，具有巨大的经济和营养价值。枣是由其野生祖先野枣（Z. jujuba var. spinosa）驯化而来，具有很高的药用价值。在这里，我们使用多种测序策略的组合，报告了干食‘君枣’枣 (JZ) 和野生枣种质 (SZ) 的 767.81Mb 和 759.24 Mb 单倍型解析组装。每个组装在端粒到端粒 (T2T) 水平上产生两个完整的单倍型解析基因组，并且在 JZ 和 SZ 内的两个单倍型之间分别发现了约 81.60Mb 和 69.07Mb 的结构变异 (SV)。比较基因组分析显示，JZ 和 SZ 之间的每条 3 号和 4 号染色体上都存在较大倒位，并且许多基因受到 SV 的影响，其中一些与淀粉和蔗糖代谢相关。对672份材料的大规模种群分析表明，酸枣起源于黄河下游，最初在当地驯化，同时在黄河中游的晋陕峡谷广泛传播并独立驯化。 。此外，我们还发现了一些新的基因组选择信号，例如组织发育、授粉、与枣树驯化相关的树体大小、受精等。总之，我们的研究提供了枣和酸枣的高质量参考基因组和新的见解。深入了解枣的驯化历史。