Abstract
The first complete chloroplast genome (cpDNA) sequence of Cinnamomum longipetiolatum was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 158,603 bp in length, contains a large single copy region (LSC) of 89,386 bp and a small single copy region (SSC) of 18,181 bp, which were separated by a pair of inverted repeats (IR) regions of 25,511 bp. The genome contains 129 genes, including 84 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 39.0%, and the corresponding values of the LSC, SSC, and IR regions are 37.7%, 33.9%, and 43.0%, respectively. Further phylogenomic analysis showed that C. longipetiolatum clustered in a clade in genus Cinnamomum.
Keywords: Cinnamomum longipetiolatum, chloroplast, Illumina sequencing, phylogenetic analysis
Cinnamomum longipetiolatum is the species of the genus Cinnamomum within the family Lauraceae. It is distributed in the south and southeast of Yunnan in China. Cinnamomum is used as spice and medicine (Sriramavaratharajan et al. 2016). Cinnamomum essential oils possess many biological activities such as anti-microbial, anti-parasitic, anti-inflammatory, antioxidant, antihyperglycemic, anti-diabetic, antitumour, and so on (Ranasinghe et al. 2013). Furthermore, camphor has been reported in the C. longipetiolatum (Thang et al. 2008). So, C. longipetiolatum is an economically significant plant having great exploitation potentiality; however, there has been no genomic studies on C. longipetiolatum.
Herein, we reported and characterized the complete C. longipetiolatum plastid genome (MN698965). One C. longipetiolatum individual (specimen number: 5309270720) was collected from Cangyuan, Yunnan Province of China (23°18′43″ N, 99°14′52″ E). The specimen is stored at Yunnan Academy of Forestry Herbarium, Kunming, China, and the accession number is YAFH0012762. DNA was extracted from its fresh leaves using DNA Plantzol Reagent (Invitrogen, Carlsbad, CA, USA).
Paired-end reads were sequenced using Illumina HiSeq system (Illumina, San Diego, CA). In total, about 20.2.4 million high-quality clean reads were generated with adaptors trimmed. Aligning, assembly, and annotation were conducted by CLC de novo assembler (CLC Bio, Aarhus, Denmark), BLAST, GeSeq (Tillich et al. 2017), and GENEIOUS v 11.0.5 (Biomatters Ltd, Auckland, New Zealand). To confirm the phylogenetic position of C. longipetiolatum, other four species of genus Cinnamomum from NCBI were aligned using MAFFT v.7 (Katoh and Standley 2013). The Auto algorithm in the MAFFT alignment software was used to align the five complete genome sequences and the G-INS-i algorithm was used to align the partial complex sequences. The maximum-likelihood (ML) bootstrap analysis was conducted using RAxML (Stamatakis 2006); bootstrap probability values were calculated from 1000 replicates. Alseodaphne gracilis (MG407593) and Alseodaphne huanglianshanensis (MG407594) were served as the out-group.
The complete C. longipetiolatum plastid genome is a circular DNA molecule with the length of 158,603 bp, contains a large single copy region (LSC) of 89,386 bp and a small single copy region (SSC) of 18,181 bp, which were separated by a pair of inverted repeats (IR) regions of 25,511 bp. The overall GC content of the whole genome is 39.0%, and the corresponding values of the LSC, SSC, and IR regions are 37.7%, 33.9%, and 43.0%, respectively. The plastid genome contained 129 genes, including 84 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis showed that C. longipetiolatum clustered in a unique clade in genus Cinnamomum (Figure 1). The determination of the complete plastid genome sequences provided new molecular data to illuminate the genus Cinnamomum evolution.
Figure 1.
The maximum-likelihood tree based on the 5 chloroplast genomes of Cinnamomum genus. The bootstrap value based on 1000 replicates is shown on each node.
Funding Statement
This work was supported by Specific funds for the Fourth National Survey on Chinese Materia Medica Resources [GZY-KJS-2018-004].
Disclosure statement
No potential conflict of interest was reported by the authors.
References
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ranasinghe P, Pigera S, Premakumara GS, Galappaththy P, Constantine G R, Katulanda P. 2013. Medicinal properties of ‘true’ cinnamon (Cinnamomum zeylanicum): a systematic review. BMC Complement Altern Med. 13(1):275–284. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sriramavaratharajan V, Stephan J, Sudha V, Murugan R. 2016. Leaf essential oil of Cinnamomum agasthyamalayanum from the Western Ghats, India—a new source of camphor. Industr Crops Produ. 86:259–261. [Google Scholar]
- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):2688–2690. [DOI] [PubMed] [Google Scholar]
- Thang TD, Dai DN, Huy DQ, Dung NX. 2008. A new natural source of Camphor from Cinnamomum longepetiolatum Costerm. apud Phamh. in Vietnam. VNU J Sci Natl Sci Technol. 24:211–213. [Google Scholar]
- Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq-versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. [DOI] [PMC free article] [PubMed] [Google Scholar]