Supporting data for "The <i>Capparis spinosa</i> var. <i>herbacea</i> genome provides the first genomic instrument for diversity and evolution study of Capparaceae family"

<i>Capparis spinosa</i> L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. We sequenced and assembled the <i>Capparis spinosa</i> var. <i>herbacea</i> (Willd.) (NCBI:txid2717819) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28%, and transposable element sequences accounted for 43.98%. The proportion of tandem repeats in the <i>C. spinosa</i> var. <i>herbacea</i> genome was much higher than the average of 8.55% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82% being functionally annotated. The result of species divergence times showed that <i>C. spinosa</i> var. <i>herbacea</i> and <i>Tarenaya hassleriana</i> separated from a common ancestor 43.31 MYA. This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled <i>C. spinosa</i> var. <i>herbacea</i> genome might provide a system for studying the diversity, speciation, and evolution of this family, and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.