Advances of genome sequencing and its applications in Chinese jujube (Ziziphus jujuba Mill.)

Genome-sequencing is a key to crack genetic code and is of significant strategic value to the molecular improvement of plants. Chinese jujube (Ziziphus jujuba Mill.), a major dry fruit and a traditional Chinese herbal medicine, is the most valued member of family Rhamnaceae. We carried out the de novo genome-sequencing of Z. jujuba Mill. ‘Dongzao’ in 2010, and published the first whole genome sequence of jujube and Rhamnaceae in 2014. The genome of Chinese jujube is relatively small (444 Mb), but is of high complexity in terms of high heterozygosity (1.9%), densely and evenly distributed SSR (378.1 Mb) as well as low GC content (33.41%). A total of 32,808 protein-encoding genes comprising 3,084 jujube-specific genes were predicted, of which 23,996 ones were anchored to the 12 pseudo-chromosomes constructed by the aid of a high density SNP genetic map. The jujube genome underwent frequent inter-chromosome fusions and segmental duplications but no recent whole-genome duplication. Comprehensive phylogenetic analysis basing on genome sequences supported the transfer of family Rhamnaceae from order Rhamnales into Rosales. Comparative genome analysis coupled with transcriptome and re-sequencing data revealed the molecular mechanisms underlining some of the jujube’s distinct properties including extreme accumulation of ascorbic acid (vitamin C) and sugar in fruit, and self-pruning shoot growing habit. In addition, genome-wide screening of SSR markers, reference genes, MADS-box genes and MAPK gene family have been carried out in jujube. In the near future, genome wide association study (GWAS), multi-omics analysis and genome-assisted breeding will greatly promote both the basic and applied research in jujube.