<i>Ziziphus jujuba</i> genome assembly and annotation

The jujube (Ziziphus jujuba Mill.), a member of the Rhamnaceae family, is a major perennial fruit crops with enormous productive, ecological as well as traditional herbal values. Here, we present the population structure, genetic diversity, genomic variations of a diverse collection of 1,057 jujube accessions. We de novo assembled four high-quality jujube genomes and constructed a gene-based pan-genome coupling with two previously released genomes. Among pan-genome, a large number of genomic variations encompassing SNP, InDel and SVs were identified. Especially, a MADS-box family gene ZjFGD1 harboring a 12-bp InDel underlies flowering time and fruit ripening. Graph-based genome enables us to perform SV-based GWAS for 17 horticultural traits and identified 109 associated SVs. Notably, a 2.3-kb PAV in the upstream of ZjMED12 was strong associated with seed-setting rate and knocking out of ZjMED12 ortholog in rice led to low seed-setting rate. Integrating SNP-based GWAS, expression analysis and transgenic validation, we identified a causal gene ZjCDKI5, which pleiotropically regulates bearing-shoot length and leaf size in jujube. Our study not only illuminates the genetic basis of key domestication traits, but also provides a deep and rich genomic resource to promote hypothesis-driven basic research and genomics-assisted crop improvement for this unique perennial fruit tree.