The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species

Abstract

Cinnamomum camphora, a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized as herbal medicines and essential oils. Here, we reported the complete sequencing of the chloroplast genome of Cinnamomum camphora using illumina technology. The chloroplast genome of Cinnamomum camphora is 152,570 bp in length and characterized by a relatively conserved quadripartite structure containing a large single copy region of 93,705 bp, a small single copy region of 19,093 bp and two inverted repeat (IR) regions of 19,886 bp. Overall, the genome contained 123 coding regions, of which 15 were repeated in the IR regions. An analysis of chloroplast sequence divergence revealed that the small single copy region was highly variable among the different genera in the Lauraceae family. A total of 40 repeat structures and 83 simple sequence repeats were detected in both the coding and non-coding regions. A phylogenetic analysis indicated that Calycanthus is most closely related to Lauraceae, both being members of Laurales, which forms a sister group to Magnoliids. The complete sequence of the chloroplast of Cinnamomum camphora will aid in in-depth taxonomical studies of the Lauraceae family in the future. The genetic sequence information will also have valuable applications for chloroplast genetic engineering.

Keywords: Chloroplast genome; Cinnamomum camphora; Illumina sequencing; Lauraceae; Phylogeny.

Figure 1. Gene map of the Cinnamomum camphora chloroplast genome.

Genes lying inside of the molecule are transcribed in the clockwise direction, where as those outside are transcribed in the counterclockwise direction. Genes are color-coded based on their functional category. The innermost circle denotes the GC content across the genome. The dark gray inner circle corresponds to the GC content, and the light gray corresponds to the AT content of the genome. Large single copy (LSC), small single copy (SSC) and inverted repeat (IRA and IRB) regions are indicated.

Figure 2. Comparison of the nucleotide variability (Pi) values of the whole plastomes in the (A) Cinnamomum and (B) Lauraceae (window length: 600 bp, step size: 200 bp).

X-axis: positions of the midpoints of a window, Y-axis: nucleotide diversity in each window.

Figure 3. Number and type of repeated sequences in five plastomes of Lauraceae.

(A) Frequencies of the palindromic repeats by length; (B) frequencies of the tandem repeats by length; (C) frequencies of the forward repeats by length; (D) total of the three repeat types.

Figure 4. Number and type of simple sequence repeats (SSRs) in five plastomes of Lauraceae.

(A) Numbers of different SSR types identified in the five Lauraceae chloroplast genomes and (B) frequencies of identified SSR motifs in different repeat class types. SSRs were classified as the number of repeat unit lengths.

Figure 5. Molecular phylogenetic tree of 26 species based on a neighbor joining analysis.

Numbers above and below nodes are bootstrap support values ≥50%.