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, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication. A balanced sweetness and acidity taste is among the most important characteristics of fruits. It is generally believed that human selection of sweetness plays a crucial role in the process of domestication from wild to cultivated fruit trees. However, the molecular mechanisms underlying fruit taste domestication still remain unclear. It is also unclear whether taste improvement is mainly determined by positive selection of advantageous traits such as sweetness or negative selection of disadvantageous trait such as acidity. Chinese jujube, domesticated from the wild jujube, is an economically important fruit tree crop in China. In this study, we sequenced and assembled the genome of a dry jujube and analyzed the genetic relationship between cultivated and wild jujubes through genome resequencing. Key genes involved in the acid and sugar metabolism were identified in the selective sweep regions. This finding suggested an important domestication pattern in fruit taste and also provided insights into the fruit molecular breeding and improvement.

The Ethylene response factor (ERF) belongs to the APETALA2/ethylene response factor (AP2/ERF) superfamily, located at the end of the ethylene signalling pathway, and has important roles in regulating the ethylene-related response genes. Thus, identifying and charactering this transcription factor would be helpful to elucidate ethylene related fruit ripening regulation in Chinese jujube (Ziziphus jujuba Mill.). In the present study, 119 AP2/ERF genes, including 5 Related to ABI3/VPs (RAV), 17 AP2s, 57 ERFs, 39 dehydration-responsive element-binding (DREB) factors and 1 soloist gene, were identified from the jujube genome sequences. Genome localization, gene duplication, phylogenetic relationships and conserved motifs were simultaneously analysed. Using available transcriptomic data, 85 genes with differential transcripts in the flower, leaf and fruit were detected, suggesting a broad regulation of AP2/ERF genes in the growth and development of jujube. Among them, 44 genes were expressed in the fruit. As assessed by quantitative PCR, 15 up- and 23 downregulated genes corresponding to fruit full maturity were found, while in response to 100 μl l⁻¹ ethylene, 6 up- and 16 downregulated genes were generated. By comparing the output, ZjERF54 and DREB39 were found to be the best candidate genes that positively participated in jujube fruit ripening, while ZjERF25 and ZjERF36, which had an ERF-associated amphiphilic repression (EAR) motif, were ripening repressors. These findings help to gain insights into AP2/ERF gene evolution and provide a useful resource to further understand the ethylene regulatory mechanisms underlying Chinese jujube fruit ripening.

Chinese jujube (Ziziphus jujuba Mill.) fruit are much admired for their unique flavor and high nutritional value. This study tracks changes in skin color and antioxidant activity over six stages (S1 … S6) of fruit development in two cultivars of jujube, ‘Junzao’ and the color mutant ‘Tailihong’. The study records the changing levels of chlorophylls, carotenoids, anthocyanins, and phenolic compounds during fruit development. Contents of chlorophylls, β-carotenes and anthocyanins decreased throughout the developmental stages in two jujube cultivars, while lutein contents decreased at first and then increased to a maximum at S6. The levels of total phenolics, total flavonoids, total flavanols, total anthocyanins, procyanidin B1, procyanidin B2, procyanidin B3, (+)-catechin, quercetin, and ferulic acid are significantly higher in ‘Tailihong’ than in ‘Junzao’ before the onset ripening (before S3). However, after S3 the level differences of these components in the two cultivars are not significant. In both cultivars, antioxidant activity reduces gradually throughout fruit development. Our findings indicate how the skin color of jujube fruit during maturation is due to changes in the levels of flavonoids, carotenoids, and anthocyanins. The color changes are also associated with changes in antioxidant activity.