Abstract
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.
Highlights
Chinese jujube (Ziziphus jujuba Mill.) (2n = 2x = 24), native to China, is one of the oldest cultivated fruit trees, with more than 7,000 years of domestication history [1]
By comparing the fresh (‘Dongzao’) and dry (‘Junzao’) jujube genomes, we found gene families involved in cell wall modification were largely expanded in ‘Junzao’, which might characterize the difference in fruit quality between dry and fresh cultivars
We reconstructed eight putative protochromosomes of the common ancestor of Rhamnaceae and Rosaceae based on the genome sequences of jujube, peach and apple, which elucidated the evolutionary processes that have shaped the genome structures of modern jujubes
Summary
Chinese jujube (Ziziphus jujuba Mill.) (2n = 2x = 24), native to China, is one of the oldest cultivated fruit trees, with more than 7,000 years of domestication history [1]. It belongs to the Rhamnaceae family in the Rosales order. The domestication mechanism of fruit sweetness and acidity taste from their wild relatives is still not well characterized. Characterization of the sugar and acid metabolism of domesticated and wild jujubes through genome-wide analyses would help elucidate the genomic mechanism underlying fruit sweetness and acidity taste improvement
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