Characterization of the complete chloroplast genome of the vulnerable agarwood tree, Aquilaria yunnanensis (Thymelaeaceae)

Aquilaria yunnanensis S. C. Huang is a precious agarwood tree endemic to Yunnan Province of China. It is included in Category II of CITES. In this study, we reported its complete chloroplast genome de novo assembled from Illumina pair-end sequencing data. The plastome was a quadripartite circular with 174,885 bp in length, including one large single copy (LSC) region of 87,508 bp and one very short small single copy (SSC) region of 3351 bp, separated by two extremely expanded inverted repeat (IR) regions of 42,013 bp. The overall GC content of the genome was 36.7%, and the corresponding values of the LSC, SSC and IR regions were 34.9, 29.1 and 38.8%, respectively. The chloroplast genome encoded 142 genes, including 96 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis revealed that sampled species of Thymelaeaceae formed a monophyletic clade, in which A. yunnanensis and A. sinensis formed a sister clade to Daphne kiusiana.