Complete chloroplast genome of Cinnamomum japonicum (Laurales: Lauraceae), an endangered tree species

Cinnamomum japonicum , belonging to family Lauraceae, is an endangered species in China. Here, the complete chloroplast (cp) genome of C. japonicum was de novo assembled using Illumina sequencing data for the first time. The whole cp genome was 152,731 bp in length, containing a pair of inverted repeat (20,092 bp for each), a large single copy (93,698 bp) and a small single copy (18,849 bp) regions. The cp genome encoded 123 genes, including 78 protein-coding genes (74 unique), 36 tRNA genes (30 unique), 8 rRNA genes (4 unique) and 1 pseudogene. The nucleotide composition was asymmetric (30.0% A, 19.7% C, 19.5% G and 30.8% T) with an overall GC content of 39.2%. The maximum likelihood phylogenetic analysis based on 19 complete cp genome sequences showed that C. japonicum was closely related to Cinnamomum verum . This result will provided useful genomic data both for the phylogenetic research of genus Cinnamomum and the conservation of this endangered species.