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.