Abstract
Zygophyllum xanthoxylon and Z. fabago are two important desert plants from Zygophyllaceae, which are both widely distributed in north-western China. Here, we report the complete chloroplast genome sequences of Z. xanthoxylon and Z. fabago, which are 109,577 bp and 108,695 bp in length, respectively. The inverted repeat regions, the large single-copy region and the small single-copy region of Z. xanthoxylon are 5084 bp, 83,735 bp, and 15,674 bp in length, respectively, while those of Z. fabago are 4669 bp, 82,293 bp and 17,064 bp in length, respectively. A total of 98 genes were annotated in the genome of Z. xanthoxylon including 29 tRNA, 4 rRNA and 65 protein-coding genes, and 100 genes were annotated in the genome of Z. fabago including 31 tRNA, 4 rRNA and 65 protein-coding genes. Phylogenetic analysis showed Z. xanthoxylon clustered and Z. fabago formed a monophyletic group sister to Tetraena mongolica.