Characterization of the complete chloroplast genome of Cephalotaxus sinensis (Cupressales: Taxaceae), an endangered Tertiary relict tree endemic to China

Technical Note
  • 32 Downloads

Abstract

Cephalotaxus sinensis is an endangered Tertiary relict tree endemic to China with high medicinal values. To contribute to its conservation genetics studies, its complete chloroplast (cp) genome was assembled using Illumina high-throughput sequencing technology in this study. The cp genome is 135,646 bp long with an asymmetric base composition (32.5% A, 17.6% C, 17.5% G and 32.4% T). It encodes a set of 113 unique genes (incl. 82 protein coding, 27 tRNA and 4 rRNA genes) with one of them (trnQ-UUG) being duplicated. Besides, 14 genes (atpF, ndhA, ndhB, petB, petD, rpl2, rpl16, rpoC1, rps12, rps16, trnA-UGC, trnG-UCC, trnI-GAU and trnK-UUU) possess a single intron, and another gene (ycf3) has a couple of introns. Phylogenetic analysis generally supported the current family-level taxonomy of the order Cupressales, and suggested that C. sinensis is closely related to the congeneric C. oliveri.

Keywords

Cephalotaxus sinensis Chloroplast genome MITObim Phylogenetic analysis 

Notes

Acknowledgements

This study was financially supported by grants from the Anhui Provincial Natural Science Foundation (1608085MC63) and Anhui Provincial Key Project of Higher Education Institutions for Excellent Visiting Scholar (gxfxZD2016172).

Supplementary material

12686_2018_1033_MOESM1_ESM.doc (106 kb)
Supplementary material 1 (DOC 105 KB)

References

  1. Chongqing Municipal Government (2015) Checklist of protected key wild plants in Chongqing Municipality (batch I). http://www.cq.gov.cn/publicinfo/web/views/Show!detail.action?sid=3961034. Accessed 2 Feb 2018
  2. Farjon A, Rushforth K, Christian T (2013) Cephalotaxus sinensis. The IUCN Red List of Threatened Species 2013:e.T42200A2960468.  https://doi.org/10.2305/IUCN.UK.2013-1.RLTS.T42200A2960468.en
  3. Fu L, Li N, Mill RR (1999) Cephalotaxaceae. Flora China 4:85–88Google 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. Nucl Acids Res 41:e129.  https://doi.org/10.1093/nar/gkt371 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Li W, Dai RJ, Yu YH, Li L, Meng WW, Deng YL (2007) Two new flavonoid diglycosides from Cephalotaxus sinensis. Chin Chem Lett 18:837–839.  https://doi.org/10.1016/j.cclet.2007.05.018 CrossRefGoogle Scholar
  6. Liu Y-H, Xu Z-R (1996) Checklist of precious plants in Fujian Province. For Prospect Des 1996:57–62Google Scholar
  7. 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. Nucl Acids Res 41:W575–W581.  https://doi.org/10.1093/nar/gkt289 CrossRefGoogle Scholar
  8. Luo C-W, Wang X-Q, Ge J-W (1994) Precious tree species in Hubei Province. Hubei For Sci Technol 1994:45–49Google Scholar
  9. Si Q, Zang D, Fu J, Liu J (2016) Study on causes of dormancy and methods for breaking dormancy of Cephalotaxus sinensis (Rehd. & Wils.) Li seeds. Shandong Agric Sci 48:42–44, 48.  https://doi.org/10.14083/j.issn.1001-4942.2016.05.011 Google Scholar
  10. Sun W-J, Mei G-P, Li J-M (2011) Revision of key protected plants list in Henan Province. J Henan Agric Univ 45:358–361.  https://doi.org/10.16445/j.cnki.1000-2340.2011.03.003 Google Scholar
  11. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol 30:2725–2729.  https://doi.org/10.1093/molbev/mst197 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Yi X, Gao L, Wang B, Su Y-J, Wang T (2013) The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of Cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms. Genome Biol Evol 5:688–698.  https://doi.org/10.1093/gbe/evt042 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Zhu M-Q, Bian Y, Su J (2005) Study on the diversity of endophytic fungi on Cephalotaxus sinensis. J Northwest Sci-Tech Univ Agric For (Nat Sci Ed) 33:264.  https://doi.org/10.13207/j.cnki.jnwafu.2005.s1.076 Google Scholar

Copyright information

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

Authors and Affiliations

  1. 1.College of Life SciencesAnqing Normal UniversityAnqingPeople’s Republic of China
  2. 2.Anhui Key Laboratory for Biodiversity Studies and Ecological Conservation in Southwestern Anhui ProvinceAnqingPeople’s Republic of China

Personalised recommendations