The complete chloroplast genome ofCinnamomum camphoraand its comparison with relatedLauraceaespecies

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.

The complete chloroplast genomes of the evergreen tree species Cinnamomum camphora and Cinnamomum parthenoxylon (Laurales: Lauraceae)

“…As expected, the five Cinnamomum taxa were more closely related to one another than to the others. However, surprisingly, the cp genome of C. camphora obtained in this study (MH050970) was found to be more closely related to that of C. parthenoxylon than to those two previously reported cp genomes of C. camphora (LC228240; MF156716) (Chen et al 2017;Wu, Wang et al 2017). It should be noted that the two more closely related cp genomes of C. camphora (MH050970; LC228240) possess the identical genomic organization, while the small single-copy (SSC) region of the relatively distant one (MF156716) displays an opposite direction.…”

“…After trimming with Trimmomatic v0.36 (Bolger et al 2014), 12.6 M and 4.6 M of 150-bp paired raw reads were employed for assembling the cp genomes using MITObim v1.9 (https://github.com/chrishah/MITObim) (Hahn et al 2013), with that of Cinnamomum micranthum (KR014245) (Wu et al 2016) as the reference. Genome annotation was done with the CpGAVAS web server (Liu et al 2012), and was delicately adjusted by comparing with those annotated cp genomes of their congeners (Wu et al 2016;Chen et al 2017;.…”

Introductory Chapter: Transgenics—Crops Tailored for Novel Traits

“…The second genome is the chloroplast genome, the plastome that has been modified in a number of plant species, including model, crop, and tree plants. Plastome is a doublestranded DNA molecule of 152 (Cinnamomum campohra) -218 kb (Pelargonium) size [15,16]. Approximately, 120 genes in various plant species are encoded by the plastome [17].…”

Incongruence of morphological determinations and DNA barcode sequences: a case study in Cinnamomum (Lauraceae)

“…Commonly applied chloroplast DNA barcode markers (psbA-trnH intergenic spacer, trnK intron including the matK gene, trnL-trnF region; Hollingsworth & al. 2011;Liu & al. 2017) and the less frequently used trnQ-rps16 intergenic spacer obtained by Sanger sequencing likewise confirmed C. camphora.…”