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In this study, the chloroplast (Cp) genome of  Zanthoxylum avicennae  (Lam.) DC was sequenced by high-throughput sequencing technology. The length of the Cp genome of  Zanthoxylum avicennae  was 158,568 bp, and the total GC content was 38.4%, including a large single-copy (LSC) region of 86,318 bp, a small single-copy (SSC) region of 18,250 bp, and 27,000 bp of inverted repeats (IRs). The Cp genome encoded 131 genes, including 88 protein-coding, 37 tRNA, and six rRNA genes. Phylogenetic analysis of the genome sequence showed that  Zanthoxylum avicennae  was closely related to  Zanthoxylum nitidum ,  Zanthoxylum esquirolii  and  Zanthoxylum motuoense  of the Rutaceae family.

Complete chloroplast genome of Zanthoxylum avicennae (Lam.) DC (Rutaceae: Zanthoxylum )