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Conservation Genetics Resources

, Volume 11, Issue 3, pp 267–269 | Cite as

Complete chloroplast genome of Cinnamomum japonicum (Laurales: Lauraceae), an endangered tree species

  • Xiaolong Ren
  • Chao Yang
  • Guiliang Xin
  • Xiaomin Du
  • Guolun Jia
  • Nan Hao
  • Huidong Liu
  • Wenzhe LiuEmail author
Technical Note
  • 138 Downloads

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.

Keywords

Cinnamomum japonicum Chloroplast genome Endangered species Phylogenetic analysis 

Notes

Acknowledgements

This study was financially supported by the National Natural Science Foundation of China (31770413).

References

  1. Cai JX, You ZQ, Huang XD, Wu ZS (2006) Bioactive essential oils from Cinnamomum japonicum Sibe. J Trop Subtrop Bot 14(5):403–408Google Scholar
  2. Fu LK (1992) China plant red data book—rare and endangered plants. Science Press, BeijingGoogle Scholar
  3. Gu XR, Pan JJ (2005) Formation of in vitro cultyure system for Cinnamomum japonicum Sieb. J Southwest Agric Univ 27(6):825–828Google Scholar
  4. 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):e129CrossRefGoogle Scholar
  5. 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-W581CrossRefGoogle Scholar
  6. Nitta I, Ohsawa M (2001) Geographical transition of sylleptic/proleptic branching in three Cinnamomum species with different bud types. Ann Bot 87(1):35–45CrossRefGoogle Scholar
  7. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313CrossRefGoogle Scholar
  8. World Conservation Monitoring Centre (1998) Cinnamomum japonicum. The IUCN Red List of Threatened Species 1998: e.T32390A9696302Google Scholar
  9. 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):1024–1031Google Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life ScienceNorthwest UniversityXi’anChina

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