The complete chloroplast genome of <i>Malus komarovii</i> (Rosaceae)

<i>Malus komarovii</i> (Sarg.) Rehder is an endangered species endemic to China. Using Deep Genome Skimming (DGS) data, we assembled the complete chloroplast genome, which is 159,982 bp in length and comprises a Large Single-Copy (LSC, 88,119 bp), a Small Single-Copy (SSC, 19,157 bp), and two Inverted Repeats (IR, 26,353 bp each). The genome encodes 131 genes, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analyses show that <i>M. komarovii</i> forms a distinct lineage among the seven major clades, indicating pronounced genetic distinctiveness and potential value as a germplasm resource for breeding. This chloroplast genome provides valuable data for future studies on species identification and phylogenetic relationships within <i>Malus</i>.