Analysis on chloroplast genomic characteristics of Cinnamomum bodinieri

Cinnamomum bodinieri is important landscaping and economic tree species, which is rich in essential oils in branches and leaves. However, there are few theoretical researches on the genomics of C. bodinieri. In order to reveal the chloroplast genomic characteristics and phylogenetic relationship of C. bodinieri, the complete chloroplast genome was sequenced based on Illumina platform and assembled through de novo. The genome structure, gene composition, sequence repeats, codon usage bias and phylogeny were analyzed subsequently. Furthermore, the phylogenetic tree was constructed with the chloroplast genome data of the main species of Subfam. Lauroideae. The results were as follows: (1) The complete chloroplast genome of C. bodinieri was 152 727 bp in length including two inverted repeats (IRs) of 20 132 bp, which were separated by large single copy(LSC) of 93 605 bp and short single copy(SSC) of 18 858 bp, respectively, and the GC content was 39.13%. (2) The genome encoded 127 functional genes, including 83 protein-coding genes (PCGs), 36 tRNA genes, and 8 rRNA genes. A total of 92 SSR loci were detected in the chloroplast genome, and most of them were composed of nucleobase A and T. The codon adaptation index (CAI) and effective number of codons (ENc) were 0.166 and 54.68, respectively. There were some differences in IR region and the boundary of two SC regions of the chloroplast genomes between C. bodinieri and related species. (3) Phylogenetic tree based on 24 species of Subfam. Lauroideae showed that the C. bodinieri was most closely related to C. camphora. The phylogeny strongly supported the establishment of the three clades, Cinnamomum-Ocotea, Laurus-Neolitsea, and Machilus-Persea. This study enriched the information on the genetic resources of C. bodinieri, and further clarified the phylogenetic status of the main genera of Subfam. Lauroideae.