Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature

Abstract

Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes #3 in D1, #1 in D2, and #4 in wild. Genes under the most significant selection on chromosomes #4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.

Identification and expression analysis of BURP domain-containing genes in jujube and their involvement in low temperature and drought response

“…A total of 17 BURP genes were identified in 'Junzao' genome, and the variation of length of these sequences suggested high complexity within the ZjBURP gene family, as also reported in Medicago [35]. In addition, the genome sequences of 'Dongzao' and 'Wild jujube' have also been reported recently [36,37]; therefore, we can obtain more insight into the synteny and evolution of BURP gene family among wild, fresh, and dry jujube. Moreover, the chromosomal location of ZjBURPs in 'Junzao' genome may also provide clues for the formation and evolution of this gene family in jujube.…”

Convergent evolution of plant prickles is driven by repeated gene co-option over deep time

“…Mining additional genomic data for LOG mutations co-occurring with losses of prickles in other eudicot lineages, we found that the fruit-bearing tree crop jujube, commonly known as Chinese date (Ziziphus jujuba), in the Rhamnaceae family, carried two independent mutations (a 1 bp deletion and an exonic insertion) in a LOG homolog in two cultivars with suppressed prickles (also known as stipular spines) (Fig. 4B) (17)(18)(19). Importantly, neither mutation was found in Sour jujube (Z. jujuba var.…”

Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube

“…So far four versions of the genome assembly of jujube, including Z. jujuba ‘Dongzao’ [ 14 , 15 ] (DZV1, DZV2), Z. jujuba ‘Junzao’ [ 4 ] (JZV1) and Z. jujuba var. spinosa ‘Suanzao’ [ 16 ] (SJV1), has been achieved. These reported draft jujube genomes still contain a large number of unclosed gaps and fragmented unanchored sequences [ 4 , 14 , 16 ].…”