Sequencing the chloroplast genome of a jujube genotype (Ziziphus jujuba Mill. 'Fengmiguan') uncovered a 101 bp insertion in the large-single copy region.

Ziziphus jujuba Mill., commonly referred to as jujube, is a species of fruiting buckthorn (family Rhamnaceae) that is frequently found across the Shaanxi, Shanxi, and Hebei provinces of China. The 'Fengmiguan' variety of jujube, also known as 'Honey jar,' is distinguished by its high yield and sugar content, as well as its strong ability to adapt to different environments. In this study, we sequenced and assembled the chloroplast genome (i.e. the plastome) of 'Fengmiguan' jujube using a paired-end short-read sequencing technique. The plastome exhibits a quadripartite structure with a total length of 161,818 bp that consists of a large single-copy region (89,427 bp), a small single-copy region (19,361 bp), and two inverted repeats (26,515 bp). The GC content of the plastome is 36.75%. Annotation of the 'Fengmiguan' jujube plastome revealed 123 genes, including 79 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis revealed that the 'Fengmiguan' variety is closely related to the 'Bokjo' variety. Furthermore, we found four variations between these two varieties of jujube, one of which was a 101 bp insertion. Our findings enhance the current understanding of the phylogenetic relationship between different varieties of Z. jujuba Mill., which could possibly aid in the improvement of genetic breeding and population selection in jujubes.