Skip to main content

The complete chloroplast genome of Daphne kiusiana, an evergreen broad-leaved shrub on Jeju Island

Abstract

Plants of Daphne kiusiana on Jeju Island exhibit morphologically and genetically unique traits. Its taxonomic entity is still unclear and populations are decreasing in size because of human activity. Taxonomic delimitation and conservation efforts are required at the genomic level. We determined the complete chloroplast (cp) genome of this endangered species on Jeju Island, South Korea. Its sequence is 171,491 bp long, and comprises a pair of 41,891 bp inverted repeats, a large-single-copy (LSC) region (85,028 bp), and a diminished small-single-copy region (2681 bp). The cp genome has 135 genes, including 89 that encode proteins, plus 38 tRNAs, and eight rRNAs. Five genes (rpl32, ndhF, accD, clpP, and ndhK) are pseudogenized or lost in its cpDNA. When compared with that of a related species, Aquilaria sinensis, its LSC region contains a large inversion event between rbcL and rps12 that caused pseudogenization of clpP and accD.

This is a preview of subscription content, access via your institution.

Fig. 1

References

  • Choi IS, Kim SY, Choi BH (2013) Taxonomic position and genetic differentiation of Korean Astragalus mongholicus Bunge. Korean J Plant Taxon 43(1):12–21. doi:10.11110/kjpt.2013.43.1.12

    Article  Google Scholar 

  • Choi IS, Lee JH, Choi BH (2014) Isolation and characterization of 12 microsatellite loci from Maackia fauriei (Fabaceae), a large tree endemic to Jeju Island. Conserv Genet Resour 6(4):1027–1029. doi:10.1007/s12686-014-0277-6

    Article  Google Scholar 

  • Chung MY, Nason JD, Sun BY, Moon MO, Chung JM, Park CW, Chung MG (2010) Extremely low levels of genetic variation in the critically endangered monotypic fern genus Mankyua chejuense (Ophioglossaceae) from Korea: implications for conservation. Biochem Syst Ecol 38(5):888–896

    CAS  Article  Google Scholar 

  • Fajardo D et al (2013) Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing. Tree Genet Genomes 9(2):489–498. doi:10.1007/s11295-012-0573-9

    Article  Google Scholar 

  • Jo YS, Kim TW, Choi BJ, Oh HS (2012) Current status of terrestrial mammals on Jeju Island. J Species Res 1(2):249–256. doi:10.12651/JSR.2012.1.2.249

    Article  Google Scholar 

  • Korea National Arboretum (2008) Rare plants data book in Korea. Korea National Arboretum, Pocheon, p 100

    Google Scholar 

  • Lee JS, Lee KH, So SK, Choi CH, Kim MY (2013) A new species of Daphne (Thymelaeaceae): D. jejudoensis M. Kim. Korean J Plant Taxon 43(2):94–98. doi:10.11110/kjpt.2013.43.2.94

    Article  Google Scholar 

  • Lee JH, Lee DH, Choi IS, Choi BH (2014) Genetic diversity and historical migration patterns of an endemic evergreen oak, Quercus acuta, across Korea and Japan, inferred from nuclear microsatellites. Plant Syst Evol 300(8):1913–1923. doi:10.1007/s00606-014-1017-9

    Article  Google Scholar 

  • Lee JH, Cho WB, Yang SG, Han EK, Lyu ES, Kim WJ, Moon BC, Choi GY (2017) Development and characterization of 21 microsatellite markers in Daphne kiusiana, an evergreen broad-leaved shrub endemic to Korea and Japan. Korean J Plant Taxon 47(1):6–10. doi:10.11110/kjpt.2017.47.1.6

    Article  Google Scholar 

  • Lin CS et al (2015) The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family. Sci Rep 5:9040. doi:10.1038/srep09040

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 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:W575–W581. doi:10.1093/nar/gkt289

    Article  PubMed  PubMed Central  Google Scholar 

  • Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255. doi:10.1093/bioinformatics/bth352

    CAS  Article  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Research Foundation of Korea (NRF-2016R1C1B2012150), and a basic Grant (K17401) for the K-herb Research Center, Korea Institute of Oriental Medicine.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jung-Hyun Lee.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Cho, WB., Han, EK., Choi, G. et al. The complete chloroplast genome of Daphne kiusiana, an evergreen broad-leaved shrub on Jeju Island. Conservation Genet Resour 10, 103–106 (2018). https://doi.org/10.1007/s12686-017-0774-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12686-017-0774-5

Keywords

  • Chloroplast genome
  • Conservation
  • Daphne kiusiana
  • Jeju Island