| Summary: | The complete chloroplast genome sequence of Chaenomeles cathayensis and Chaenomeles thibetica was characterized from Illumina pair-end sequencing. The length of C. cathayensis and C. thibetica chloroplast genome of was 159,875 bp and 159,907 bp, respectively. The C. cathayensis chloroplast genome contained a large single-copy region (LSC) of 87,813bp, a small single-copy region (SSC) of 19,304 bp, and two inverted repeat (IR) regions of 26,379 bp, which is a quadripartite structure. Similarity, The C. thibetica chloroplast genome also contained a quadripartite structure, including a LSC region (87,851 bp), a SSC region (19,298 bp), and two IR regions (26,379 bp). The overall GC content of C. cathayensis and C. thibetica are both 36.57%. The C. cathayensis and C. thibetica chloroplast genome contains 130 complete genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The C. thibetica chloroplast genome contains 130 complete genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The neighbour-joining phylogenetic analysis showed that C. cathayensis and C. thibetica clustered together, indicated that C. cathayensis and C. thibetica have closed evolutionary relationship compared with other Chaenomeles species.
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