Advertisement

Horticulture, Environment, and Biotechnology

, Volume 59, Issue 1, pp 71–80 | Cite as

The complete chloroplast genome sequence of Fritillaria thunbergii Miq., an important medicinal plant, and identification of DNA markers to authenticate Fritillariae Bulbus

  • Byeong Cheol Moon
  • Inkyu Park
  • Wook Jin Kim
  • Sungyu Yang
  • Young Min Kang
Research Report
  • 180 Downloads

Abstract

The genus Fritillaria is an important herbaceous medicinal plant. The dried bulbs of many Fritillaria species are used as Fritillariae Bulbus in traditional oriental medicines. However, these herbal medicines frequently contain mixtures of different types of Fritillariae Bulbus and other Fritillaria species with little or no medicinal value. The accurate identification of different types of Fritillariae Bulbus is very difficult due to the morphological similarities between the plants and dried bulbs; therefore, it is necessary to accurately identify these herbal medicines and other Fritillaria species based on their genetic characteristics. To find molecular markers for Fritillaria species and elucidate the genomic characteristics of F. thunbergii, we sequenced the complete chloroplast (cp) genome of F. thunbergii and performed a comparative analysis with related plant taxa. The complete cp genome of F. thunbergii is 152,155 bp with a quadripartite structure, which is similar to other plants, and was highly similar to previously reported Fritillaria cp genomes in regard to gene content, order, orientation, and GC contents. Comparative analysis of the cp genomes identified two genes, matK and rps16, that contained sufficient markers to distinguish between two herbal medicines (Fritillariae Thunbergii and Fritillariae Hupehensis Bulbus) and five Fritillaria species. These results provide useful information for identification of Fritillaria species and quality control of Fritillariae Bulbus.

Keywords

Fritillaria species matK rps16 Molecular identification Marker nucleotide 

Notes

Acknowledgements

We thank the ‘Classification and Identification Committee of the KIOM’ for critical identifications, and also thank the Korean Herbarium of Standard Herbal Resources (IH code KIOM) for providing plant materials. This work was supported by the grant ‘Development of Foundational Techniques for the Domestic Production of Authentic Herbal Medicines based on the Establishment of Molecular Authentication System’ (K16403 and K17403), and by funding from the Ministry of Science, ICT, and Future Planning (MSIP) of Korea to the KIOM.

Supplementary material

13580_2018_8_MOESM1_ESM.docx (1.1 mb)
Supplementary material 1 (DOCX 1109 kb)

References

  1. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580CrossRefPubMedPubMedCentralGoogle Scholar
  2. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:12794–12797CrossRefPubMedCentralGoogle Scholar
  3. Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T et al (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE 5:e8613CrossRefPubMedPubMedCentralGoogle Scholar
  4. Dan Bensky SC, Stoger Erich, Gamble Andrew (2004) Chinese herbal medicine: materia medica. Eastlan Press, Bejing, pp 378–383Google Scholar
  5. Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17:134CrossRefPubMedPubMedCentralGoogle Scholar
  6. Delcher AL, Salzberg SL, Phillippy AM (2003) Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinform 10–13.  https://doi.org/10.1002/0471250953.bi1003s00
  7. Fan C, Li X, Zhu J, Song J, Yao H (2015) Endangered Uyghur medicinal plant Ferula identification through the second internal transcribed spacer. Evid Based Complement Altern Med 2015:479879.  https://doi.org/10.1155/2015/479879 Google Scholar
  8. FOC (Flora of China) (2017) http://www.efloras.org/florataxon.aspx?flora_id=2&taxon_id=113029/. Accessed 24 May 2017
  9. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32:W273–W279CrossRefPubMedPubMedCentralGoogle Scholar
  10. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. In: Nucleic acids symposium series 41Google Scholar
  11. Hao Z, Cheng T, Zheng R, Xu H, Zhou Y, Li M, Lu F, Dong Y, Liu X et al (2016) The complete chloroplast genome sequence of a relict conifer Glyptostrobus pensilis: comparative analysis and insights into dynamics of chloroplast genome rearrangement in Cupressophytes and Pinaceae. PLoS ONE 11:e0161809CrossRefPubMedPubMedCentralGoogle Scholar
  12. Kim W, Ji Y, Choi G, Kang Y, Yang S, Moon B (2016) Molecular identification and phylogenetic analysis of important medicinal plant species in genus Paeonia based on rDNA-ITS, matK, and rbcL DNA barcode sequences. Genet Mol Res 15:gmr.15038472Google Scholar
  13. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  14. KIOM (Korea Institute of Oriental Medicine) (2017) Defining dictionary for medicinal herbs [Korean, ‘Hanyak Giwon Sajeon’]. http://boncho.kiom.re.kr/herbarium/codex.php/. Accessed 15 Mar 2017
  15. Ku C, Hu JM, Kuo CH (2013) Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS ONE 8:e62548CrossRefPubMedPubMedCentralGoogle Scholar
  16. Kuang DY, Wu H, Wang YL, Gao LM, Zhang SZ, Lu L (2011) Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. Genome 54:663–673CrossRefPubMedGoogle Scholar
  17. Kumar S, Hahn FM, McMahan CM, Cornish K, Whalen MC (2009) Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines. BMC Plant Biol 9:131CrossRefPubMedPubMedCentralGoogle Scholar
  18. Li Q, Li Y, Song J, Xu H, Xu J, Zhu Y, Li X, Gao H, Dong L et al (2014) High-accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy. New Phytol 204:1041–1049CrossRefPubMedGoogle Scholar
  19. Li X, Su Y, Li X, Xue G, Wang Q, Shi J, Wang L, Chen S (2016) Identification of Fritillariae bulbus from adulterants using ITS2 regions. Plant Gene 7:42–49CrossRefGoogle Scholar
  20. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452CrossRefPubMedGoogle Scholar
  21. Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52:267–274.  https://doi.org/10.1007/s00294-007-0161-y CrossRefPubMedGoogle Scholar
  22. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964CrossRefPubMedPubMedCentralGoogle Scholar
  23. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18.  https://doi.org/10.1186/2047-217X-1-18 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Moon B, Kim W, Ji Y, Lee Y, Kang Y, Choi G (2016) Molecular identification of the traditional herbal medicines, Arisaematis Rhizoma and Pinelliae Tuber, and common adulterants via universal DNA barcode sequences. Genet Mol Res 15:gmr.15017064CrossRefGoogle Scholar
  25. Ni L, Zhao Z, Xu H, Chen S, Dorje G (2016) The complete chloroplast genome of Gentiana straminea (Gentianaceae), an endemic species to the Sino-Himalayan subregion. Gene 577:281–288CrossRefPubMedGoogle Scholar
  26. Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7:84CrossRefPubMedPubMedCentralGoogle Scholar
  27. Semagn K, Bjørnstad Å, Ndjiondjop M (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5:2540–2568Google Scholar
  28. Sucher NJ, Carles MC (2008) Genome-based approaches to the authentication of medicinal plants. Planta Med 74:603–623CrossRefPubMedGoogle Scholar
  29. 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
  30. Warburton PE, Giordano J, Cheung F, Gelfand Y, Benson G (2004) Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Res 14:1861–1869.  https://doi.org/10.1101/gr.2542904 CrossRefPubMedPubMedCentralGoogle Scholar
  31. Weng ML, Blazier JC, Govindu M, Jansen RK (2014) Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements repeats, and nucleotide substitution rates. Mol Biol Evol 31:645–659CrossRefPubMedGoogle Scholar
  32. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255.  https://doi.org/10.1093/bioinformatics/bth352 CrossRefPubMedGoogle Scholar
  33. Xiao P, Jiang Y, Li P, Luo Y, Liu Y (2007) The botanical origin and pharmacophylogenetic treatment of Chinese materia medica Beimu. Acta Bot Sin 45:473–487Google Scholar
  34. Xin GZ, Lam YC, Maiwulanjiang M, Chan GK, Zhu KY, Tang WL, Dong TTX, Shi ZQ, Li P et al (2014) Authentication of Bulbus Fritillariae Cirrhosae by RAPD-derived DNA markers. Molecules 19:3450–3459CrossRefPubMedGoogle Scholar
  35. Yang J-B, Tang M, Li HT, Zhang ZR, Li DZ (2013) Complete chloroplast genome of the genus Cybidium: lights into the species identification, phylogenetic implications and population genetic analyses. BMC Evol Biol 13:84CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Korean Society for Horticultural Science and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Byeong Cheol Moon
    • 1
  • Inkyu Park
    • 1
  • Wook Jin Kim
    • 1
  • Sungyu Yang
    • 1
  • Young Min Kang
    • 1
  1. 1.K-herb Research CenterKorea Institute of Oriental MedicineDaejeonRepublic of Korea

Personalised recommendations