Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
References
Cai JX, You ZQ, Huang XD, Wu ZS (2006) Bioactive essential oils from Cinnamomum japonicum Sibe. J Trop Subtrop Bot 14(5):403–408
Fu LK (1992) China plant red data book—rare and endangered plants. Science Press, Beijing
Gu XR, Pan JJ (2005) Formation of in vitro cultyure system for Cinnamomum japonicum Sieb. J Southwest Agric Univ 27(6):825–828
Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Res 41(13):e129
Lohse M, Drechsel O, Kahlau S, Bock R (2013) OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res 41(W1):W575-W581
Nitta I, Ohsawa M (2001) Geographical transition of sylleptic/proleptic branching in three Cinnamomum species with different bud types. Ann Bot 87(1):35–45
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313
World Conservation Monitoring Centre (1998) Cinnamomum japonicum. The IUCN Red List of Threatened Species 1998: e.T32390A9696302
Yang JB, Li DZ, Li HT (2014) Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol Resour 14(5):1024–1031
Acknowledgements
This study was financially supported by the National Natural Science Foundation of China (31770413).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Ren, X., Yang, C., Xin, G. et al. Complete chloroplast genome of Cinnamomum japonicum (Laurales: Lauraceae), an endangered tree species. Conservation Genet Resour 11, 267–269 (2019). https://doi.org/10.1007/s12686-018-1004-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-018-1004-5