Li Kun, Chen Ruihong, Abudoukayoumu Ayimaiti, Wei Qian, Ma Zhibo, Wang Zhengyang, Hao Qing, Huang Jian
Key Laboratory of National Forestry and Grassland Administration on Forest Cultivation on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China.
College of Horticulture, Northwest A&F University, Yangling 712100, China.
Hortic Res. 2024 Mar 7;11(5):uhae071. doi: 10.1093/hr/uhae071. eCollection 2024 May.
Chinese jujube ( 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 ( var. ), and both have high medicinal value. Here we report the 767.81- and 759.24-Mb haplotype-resolved assemblies 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 ~81.60 and 69.07 Mb of structural variations were found between the two haplotypes within JZ and SZ, respectively. Comparative genomic analysis revealed a large inversion on each of chromosomes 3 and 4 between JZ and SZ, and numerous genes were affected by structural variations, 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 the Yellow River and was initially domesticated at local sites. It spread widely and was then independently domesticated at the Shanxi-Shaanxi Gorge of the middle Yellow River. In addition, we identified some new selection signals regions on genomes, which are involved in the tissue development, pollination, and other aspects of jujube tree morphology and fertilization domestication. In conclusion, our study provides high-quality reference genomes of jujube and wild jujube and new insights into the domestication history of jujube.
枣（Mill.）是中国最重要的落叶果树之一，具有很高的经济和营养价值。枣树是由其野生祖先酸枣（变种）驯化而来，二者都具有很高的药用价值。在此，我们结合多种测序策略，报告了鲜食枣品种‘骏枣’（JZ）和一个酸枣种质（SZ）的767.81 Mb和759.24 Mb的单倍型解析基因组。每个基因组在端粒到端粒（T2T）水平上产生了两个完整的单倍型解析基因组，在JZ和SZ的两个单倍型之间分别发现了约81.60 Mb和69.07 Mb的结构变异。比较基因组分析揭示了JZ和SZ的3号和4号染色体上各有一个大的倒位，许多基因受到结构变异的影响，其中一些与淀粉和蔗糖代谢有关。对672份种质的大规模群体分析表明，酸枣起源于黄河下游，最初在当地驯化。它广泛传播，然后在黄河中游的晋陕峡谷地区被独立驯化。此外，我们在基因组上鉴定了一些新的选择信号区域，这些区域涉及枣树形态和受精驯化的组织发育、授粉等方面。总之，我们的研究提供了枣和酸枣的高质量参考基因组，并为枣的驯化历史提供了新的见解。
