Two haplotype-resolved T2T reference genomes for Ziziphus jujuba and Z. jujuba var. spinosa provide new insights into the domestication of jujube

Abstract 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.