The complete chloroplast genome sequences of Zanthoxylum nitidum var. nitidum and Z. nitidum var. tomentosum

Zanthoxylum nitidum (Rutaceae Juss.) is a traditional Chinese medicine with four morphological types. We assembled their complete chloroplast genome sequences. The assembled genomes are 156,999–157,349 bp in length, including a large single copy (LSC) region of 84,064–84,455 bp, a small single copy (SSC) region of 17,582–17,651 bp and a pair of inverted repeats (IRs) of 27,631–27,659 bp. All genomes contained 133 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The GC content is 38.5%. The further phylogenetic analysis showed that Z. nitidum clade was a monophyletic group separated from other Zanthoxylum species.