Conservation Genetics Resources

, Volume 11, Issue 3, pp 299–301 | Cite as

The complete chloroplast genome of Siebold’s magnolia: Magnolia sieboldii (Magnoliaceae), a highly ornamental species with attractive aromatic flowers

  • Yifan Cui
  • Chong Li
  • Yue Zhang
  • Yuan Liu
  • Yuyao Wang
  • Dan Li
  • Fang K. DuEmail author
Technical Note


Magnolia sieboldii K. Koch (Magnoliaceae) is a tree species with high landscaping value, whose resource has been declining due to unreasonable exploitation. In this study, we sequenced, assembled and annotated the complete chloroplast (cp) genome of M. sieboldii. The length of M. sieboldii complete cp genome was 160,274 bp, with a typical quadripartite structure comprising a pair of inverted repeat regions (IRs; 26,588 bp), a large single copy region (LSC; 88,267 bp) and a small single copy region (SSC; 18,831 bp). The whole cp genome contained 111 unique genes, including 78 protein-coding genes (PCGs), 29 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. In addition, 17 genes in IRs were duplicated. The overall CG content was 39.2%. The maximum likelihood (ML) phylogenetic analysis indicated that M. sieboldii was relatively closed to the M. officinalis and M. tripetala. Our research would provide a valuable genetic resource for M. sieboldii.


Magnolia sieboldii Chloroplast genome Illumina sequencing Phylogenetic analysis 



This research was supported by the National Key Research and Development Plan “Research on protection and restoration of typical small populations of wild plants” (Grant No. 2016YFC0503106); Fundamental Research Funds for the Central Universities (Grant No. 2015ZCQ-LX-03) and National Science Foundation of China (Grant No. 41671039) to FKD.


  1. Bi GQ, Mao YX, Xing QK, Cao M (2018) HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching. Genomics 110:18–22CrossRefPubMedGoogle Scholar
  2. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772CrossRefPubMedPubMedCentralGoogle Scholar
  3. Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucl Acids Res 45:e18CrossRefPubMedGoogle Scholar
  4. Ding L, Hu WL, Wang W, Liu ZD, Li GH, Yao RS, Zhang YP, Wang G (2009) Effects of shading on the photosynthetic characteristics and growth of Magnolia sieboldii. For Resour Manag 3:61–65Google Scholar
  5. Du FG, Wang H, Liu CQ, Sun SG, Wang ZM (2006a) The research situation and conservation strategies of Magnolia Sieboldii. J Northwest Norm Univ 6:68–71Google Scholar
  6. Du FG, Wang H, Liu CQ, Yang DM, Sun SG, Wang ZM (2006b) Study on the species diversity in Magnolia sieboldii community. J Northeast Norm Univ 2:91–95Google Scholar
  7. Du FK, Lang T, Lu S, Wang Y, Li J, Yin K (2015) An improved method for chloroplast genome sequencing in non-model forest tree species. Tree Genet Genom 11:114CrossRefGoogle Scholar
  8. Khela S (2014) Magnolia sieboldii. The IUCN Red List of Threatened Species 2014: e. T194003A2293976. Accessed 15 Jan 2018
  9. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedPubMedCentralGoogle Scholar
  10. Liu C, Shi LC, Zhu YJ, Chen H, Zhang J, Lin X, Guan X (2012) CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genom 13:715CrossRefGoogle Scholar
  11. Lohse M, Drechsel O, Kahlau S, Bock R (2013) Organellar genome DRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucl Acids Res 41:W575-W581CrossRefGoogle Scholar
  12. Reuben C, Lim J (2013) Floral emblems of the World. Australian National Herbarium. Accessed 15 Jan 2018
  13. Wang JL, Wang RJ, Du FG, Sun GR, Zou K, Wang ZH, Zhang SP (2017) Genetic diversity of Magnolia sieboldii assessed with SSR markers. Acta Bot Boreal Occident Sin 2:266–272Google Scholar
  14. Xu X, Zhang J, Zheng W (2017) The complete chloroplast genome of threatened Magnolia laevifolia, a rare ornamental shrub with strong aromatic flowers. Conserv Genet Resour. CrossRefGoogle Scholar
  15. Zhang Y, Su JY, Li JQ, Du FK (2017) The complete chloroplast genome of a staple food of the giant panda, Fargesia denudata (Poaceae). Conserv Genet Resour 9:561–563CrossRefGoogle Scholar
  16. Zheng W, Xu X (2017) The complete chloroplast genome of endangered Manglietia insignis, a rare landscaping tree with red lotus-like flowers. Conserv Genet Resour. CrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  1. 1.Key Laboratory for Forest Resources and Ecosystem Processes of Beijing, College of ForestryBeijing Forestry UniversityBeijingPeople’s Republic of China
  2. 2.Forestry Bureau of BenxiBenxiPeople’s Republic of China

Personalised recommendations