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The Chinese endemic species Prunus hypoxantha is of great importance biogeographically, and is distributed in the edge of the Qinghai-Tibetan Plateau. Here, the complete chloroplast genome sequence of P. hypoxantha was assembled based on the Illumina reads. The complete plastome is 158,740 bp in length, with a large single-copy (87,206 bp) region, a small single-copy (18,884 bp) region, and two inverted repeat (26,325 bp) regions. The plastome contains 134 genes. Complete chloroplast genome sequence of P. hypoxantha will provide irreplace

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