Journal of Species Research

The National Institute of Biological Resources (국립생물자원관)
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DNA barcoding of Euphorbiaceae in Korea

  • Kim, Kyeonghee (National Institute of Biological Resources) ;
  • Park, Ki-Ryong (Department of Environmental and Energy Engineering, Kyungnam University) ;
  • Lim, Chae Eun (National Institute of Biological Resources)
  • Received : 2020.09.18
  • Accepted : 2020.11.05
  • Published : 2020.11.30
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Abstract

The Euphorbiaceae family features some of the most economically important plants that are sources of foods, oils, waxes, and medicines. The accurate identification of Euphorbiaceae species is critical in sustainable utilization of plant resources. We examined 234 sequences of nrDNA ITS, cpDNA rbcL and matK loci from 20 species in Euphorbiaceae in Korea and three outgroup taxa to develop efficient DNA barcodes. The three barcode loci were successfully amplified and sequenced for all Euphorbiaceae species. nrDNA ITS locus showed the highest mean interspecific K2P distance (0.3034), followed by cpDNA matK (0.0830), and rbcL (0.0352) locus. The degree of species resolution for individual barcode loci ranged from 75% (rbcL and matK) to 80% (ITS). The degree of species resolution was not enhanced with the different combinations of three barcode loci. The combined data set of the three loci(ITS+rbcL+matK) provided 80% of species resolution. These results confirm that ITS locus, as a single barcode, is the best option for barcoding of the Euphorbiaceae in Korea.

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References

  1. APG IV. 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181(1):1-20. https://doi.org/10.1111/boj.12385
  2. Aubriot, X., P.P. Lowry II, C. Cruaud, A. Couloux and T. Haevermans. 2013. DNA barcoding in a biodiversity hot spot: potential value for the identification of Malagasy Euphorbia L. listed in CITES Appendices I and II. Mol. Ecol. Resor. 13:57-65. https://doi.org/10.1111/1755-0998.12028
  3. Bennett, B.C. 2010. Economic Botany: Twenty-five economically important plant families. Encyclopedia of life support systems. UNESCO-EOLSS Publishers, Oxford.
  4. CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proc. Natl. Acad. Sci. USA. 106:12794-12797. https://doi.org/10.1073/pnas.0905845106
  5. China Plant BOL Group. 2011. Comparative analysis of a large dataset indicates that internal transcribed spacer(ITS) should be incorporated into the core barcode for seed plants. Proc. Natl. Acad. Sci. USA. 108:19641-19646. https://doi.org/10.1073/pnas.1104551108
  6. Choi, Y.G., J.W. Youm, C.E. Lim and S.H. Oh. 2018. Phylogenetic analysis of Viburnum (Adoxaceae) in Korea using DNA sequences. Korean J. Pl. Taxon. 48(3):206-217. https://doi.org/10.11110/kjpt.2018.48.3.206
  7. Chung, G.Y., B.-U. Oh, K.-R. Park, J.-H. Kim, M.S. Kim, G.-H. Nam and C.-G. Jang. 2003. Cytotaxonomic study of Korean Euphorbia L. (Euphorbiaceae). Korean J. Pl. Taxon. 33(3):279-293. https://doi.org/10.11110/kjpt.2003.33.3.279
  8. Croizat, L. 1945. "Euphorbia Esula" in North America. Am. Midl. Nat. 33(1):231-243. https://doi.org/10.2307/2421329
  9. Elhassan, G.O.M., A. Adhikari, O.M. Abdalla, A. Shukrulla, M.I. Choudhary, M.A. Mesaik and S. Yagi. 2015. Chemical constitutuents of Euphorbia polyacantha Boiss. and their immunomodulatory properties. Rec. Nat. Prod. 9(1):146-152.
  10. Ernst, M., O.M. Grace, C.H. Saslis-Lagoudakis, N. Nilsson, H.T. Simonsen and N. Ronsted. 2015. Global medicinal uses of Euphorbia L.(Euphorbiaceae). J. Ethnopharmacol. 176:90-101. https://doi.org/10.1016/j.jep.2015.10.025
  11. Fay, M.F., C. Bayer, W.S. Alverson, A.Y. de Bruijn and M.W. Chase. 1998. Plastid rbcL sequence data indicate a close affinity between Diegodendron and Bixa. Taxon 47(1):43-50. https://doi.org/10.2307/1224017
  12. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39(4):783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
  13. Genievskaya, Y., S. Abugalieva, A. Zhubanysheva and Y. Turuspekov. 2017. Morphological description and DNA barcoding study of sand rice (Agriophyllum squarrosum, Chenopodiaceae) collected in Kazakhstan. BMC Plant Biol. 17:177. https://doi.org/10.1186/s12870-017-1132-1
  14. Govaerts, R., D.G. Frodin, A. Radcliffe-Smith and S. Carter. 2000. World checklist and bibliography of Euphorbiaceae (and Pandaceae). Royal Botanic Gardens, Kew, Richmond.
  15. Heywood, V.H. 1985. Flowering Plants of the World. Oxford University Press, England.
  16. Hohmann, J. and J. Molnar. 2004. Euphorbiaceae diterpenes: plant toxins or promising molecules for the therapy? Acta Pharm. Hung. 74(3):149-157.
  17. Hollingsworth, P.M. 2011. Refining the DNA barcode for land plants. Proc. Natl. Acad. Sci. USA. 108(49):19451-19452. https://doi.org/10.1073/pnas.1116812108
  18. Hurusawa, I. 1940. Species generis Euphorbiae Imperi Japonici(I-IV). J. Jap. Bot. 16(6):330-461.
  19. Hurusawa, I. 1954. Eine nochmalige Durchsicht des herkommlichen Systems der Euphorbiaceen im weiteren Sinne. J. Fac. Sci. Univ. Tokyo III. 6:210-341.
  20. Jung, H.J. and K.-R. Park. 2012. Genetic and morphological divergence of Euphorbia esula and E. maackii in Korea (Euphorbiaceae). Korean J. Pl. Taxon. 42(4):267-274. https://doi.org/10.11110/kjpt.2012.42.4.267
  21. Kang, Y., Z. Deng, R. Zhang and W. Long. 2017. DNA barcoding analysis and phylogenetic relationships of tree species in tropical cloud forests. Sci. Rep. 7:12564. https://doi.org/10.1038/s41598-017-13057-0
  22. Kim, H.M., S.H. Oh, G.S. Bhandari, C.S. Kim and C.W. Park. 2014. DNA barcoding of Orchidaceae in Korea. Mol. Ecol. Res. 14(3):499-507. https://doi.org/10.1111/1755-0998.12207
  23. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120. https://doi.org/10.1007/BF01731581
  24. Kumar, S., R. Malhotra and D. Kumar. 2010. Euphorbia hirta: Its chemistry, traditional and medicinal uses, and pharmacological activities. Pharmacogn. Rev. 4(7):58-91. https://doi.org/10.4103/0973-7847.65327
  25. Kumar, S., G. Stecher, M. Li, C. Knyaz and K. Tamura. 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35(6):1547-1549. https://doi.org/10.1093/molbev/msy096
  26. Lahaye, R., M. van der Bank, D. Bogarin, J. Warner, F. Pupulin, G. Gigot, O. Maurin, S. Duthoit, T.G. Barraclough and V. Savolainen. 2008. DNA barcoding the floras of biodiversity hotspots. Proc. Natl. Acad. Sci. USA. 105(8):2923-2928. https://doi.org/10.1073/pnas.0709936105
  27. Li, B., H. Qie, J.S. Ma, H. Zhu, M.G. Gilbert, H.J. Esser, S. Dressler, P. Hoffmann, L.J. Gillespie, M. Vorontsova and G.D. McPherson. 2008. Euphorbiaceae. In: Z. Wu, H.R. Peter, D. Hong (eds.), Flora of China, vol. 11. Science Press and Missouri Botanical Garden Press, Beijing & St. Louis, pp. 288-313.
  28. Liu, Z., X. Zeng, D. Yang, G. Chu, Z. Yuan and S. Chen. 2012. Applying DNA barcodes for identification of plant species in the family Araliaceae. Gene 499(1):76-80. https://doi.org/10.1016/j.gene.2012.02.016
  29. Mishra, P., A. Kumar, A. Nagireddy, A.K. Shukia and V. Sundaresan. 2017. Evaluation of single and multilocus DNA barcodes towards species delineation in complex tree genus Terminalia. PloS One 12(8):e0182836. https://doi.org/10.1371/journal.pone.0182836
  30. Pang, X., J. Song, Y. Zhu, C. Xie and S. Chen. 2010. Using DNA barcoding to identify species within Euphorbiaceae. Planta Med. 76(15):1784-1786. https://doi.org/10.1055/s-0030-1249806
  31. Park, K.-R. and A. Backlund. 2002. Origin of the cyathium-bearing Euphorbieae (Euphorbiaceae): phylogenetic study based on morphological characters. Bot. Bull. Acad. Sinica 43(1):57-62.
  32. Park, K.-R., H.-J. Jung, J.-H. Kim, G.Y. Chung and B.-U. Oh. 2002. Comparisons of morphological and genetic diversity between endemic Euphorbia fauriei and widespread E. pekinensis (Euphorbiaceae). Korean J. Pl. Taxon. 32(2):177-191. https://doi.org/10.11110/kjpt.2002.32.2.177
  33. Park, K.-R., T. Kurosawa, M.-G. Seo, B.-E. Lee and S.-K. Ahn. 2017. Chromosome numbers of Euphorbia pekinensis complex in Far East Asia. Korean J. Pl. Taxon. 47(4):304-307. https://doi.org/10.11110/kjpt.2017.47.4.304
  34. Park, K.-R. and C.W. Park. 2015. Euphorbiaceae Juss. In: Flora of Korea Editorial Committee (ed.), Flora of Korea, vol. 5b. Junghaengsa, Inc., Seoul, pp. 74-88.
  35. Petit, R.J. and L. Excoffier. 2009. Gene flow and species delimitation. Trends Ecol. Evol. 24(7):386-393. https://doi.org/10.1016/j.tree.2009.02.011
  36. Riina, R., J.A. Peirson, D.V. Geltman, J. Molero, B. Frajman, A. Pahlevani, L. Barres, J.J. Morawetz, Y. Salmaki, S. Zarre, A. Kryukov, P.V. Bruyns and P.E. Berry. 2013. A worldwide molecular phylogeny and classification of the leafy spurges, Euphorbia subgenus Esula (Euphorbiaceae). Taxon 62(2):316-342. https://doi.org/10.12705/622.3
  37. Salatino, A., M.L. Faria Salatino and G. Negri. 2007. Traditional uses, chemistry and pharmacology of Croton species(Euphorbiaceae). J. Braz. Chem. Soc. 18(1):11-33. https://doi.org/10.1590/S0103-50532007000100002
  38. Savolainen, V., M.F. Fay, D.C. Albach, A. Backlund, M. van der Bank, K.M. Cameron, S.A. Johnson, M.D. Lledo, J.C. Pintaud, M. Powell, M.C. Sheahan, D.E. Soltis, P.S. Soltis, P. Weston, W.M. Whitten, K.J. Wurdack and M.W. Chase. 2000. Phylogeny of the eudicots: a nearly complete familial analysis based on rbcL gene sequences. Kew Bulletin 55(2):257-309. https://doi.org/10.2307/4115644
  39. Singla, A. and P. Kamla. 1990. Phytoconstituents of Euphorbia species. Fitoterapia 41(6):483-516.
  40. Sonet, G., K. Jordaens, Y. Braet, L. Bourguinon, E. Dupont, T. Backeljau, M. de Meyer and S. Desmyter. 2013. Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France. Zookeys 365:307-328. https://doi.org/10.3897/zookeys.365.6027
  41. Starr, J.R., R.F.C. Naczi and B.N. Chouinard. 2009. Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae). Mol. Ecol. Resour. 9(s1):151-163. https://doi.org/10.1111/j.1755-0998.2009.02640.x
  42. Stevens, J.R., R. Wall and J.D. Wells. 2002. Paraphyly in Hawaiian hybrid blowfly populations and the evolutionary history of anthropophilic species. Insect Mol. Biol. 11(2):141-148. https://doi.org/10.1046/j.1365-2583.2002.00318.x
  43. Swofford, D.L. 2003. PAUP*: Phylogenetic analysis using parsimony (and other methods), version 4.0a. Sinauer, Sunderland.
  44. Thakur, H.A. and D.A. Patil. 2011. Taxonomic and phylogenetic assessment of the Euphorbiaceae: A review. J. Exp. Sci. 2(3):37-46.
  45. Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL_W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673-4680. https://doi.org/10.1093/nar/22.22.4673
  46. Tokuoka, T. 2007. Molecular phylogenetic analysis of Euphorbiaceae sensu stricto based on plastid and nuclear DNA sequences and ovule and seed character evolution. J. Plant Res. 120(4):511-522. https://doi.org/10.1007/s10265-007-0090-3
  47. Tsitrone, A., M. Kirkpatrick and D.A. Levin. 2003. A model for chloroplast capture. Evolution 57(8):1776-1782. https://doi.org/10.1111/j.0014-3820.2003.tb00585.x
  48. Webster, G.L. 1986. Irritant plants in the spurge family (Euphorbiaceae). Clin. Dematol. 4(2):36-45. https://doi.org/10.1016/0738-081X(86)90062-3
  49. Webster, G.L. 1994. Classification of the Euphorbiaceae. Ann. Missouri Bot. Gard. 81(1):3-32. https://doi.org/10.2307/2399908
  50. Wells, J.D. and J.R. Stevens. 2008. Application of DNA-based methods in forensic entomology. Annu. Rev. Entomol. 53(1):103-120. https://doi.org/10.1146/annurev.ento.52.110405.091423
  51. Werle, E., C. Schneider, M. Renner, M. Volker and W. Fiehn. 1994. Convenient single-step, one tube purification of PCR products for direct sequencing. Nucleic Acids Res. 22:4354-4355. https://doi.org/10.1093/nar/22.20.4354
  52. White, T.J., T.D. Bruns, S.B. Lee and J.W. Taylor. 1990, Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: M.A. Innis, D.H. Gelfand, J.J. Sninsky and T.J. White (eds.), PCR Protocols: a guide to methods and applications. Academic Press, San Diego, pp. 315-322.
  53. Whitworth, T.L., R.D. Dawson, H. Magalon and E. Baudry. 2007. DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae). Proc. R. Soc. B 274:1731-1739. https://doi.org/10.1098/rspb.2007.0062
  54. Wurdack, K.J., P. Hoffmann and M.W. Chase. 2005. Molecular phylogenetic analysis of uniovulate Euphorbiaceae (Euphorbiaceae sensu stricto) using plastid rbcL and trnL-F DNA sequences. Am. J. Bot. 92(8):1397-1420. https://doi.org/10.3732/ajb.92.8.1397
  55. Wurdack, K.J., P. Hoffmann, R. Samuel, A. de Bruijn, M. van Der Bank and M.W. Chase. 2004. Molecular phylogenetic analysis of Phyllanthaceae (Phyllanthoideae pro parte, Euphorbiaceae sensu lato) using plastid rbcL DNA sequences. Am. J. Bot. 91(11):1882-1900. https://doi.org/10.3732/ajb.91.11.1882
  56. Yang, Y., R. Riina, J.J. Morawetz, T. Haevermans, X. Aubrio and P.E. Berry. 2012. Molecular phylogenetics and classification of Euphorbia subgenus Chamaesyce (Euphorbiacae). Taxon 64(1):764-789.
  57. Yu, J., J.H. Xue and S.L. Zhou. 2011. New universal matK primers for DNA barcoding angiosperms. J Syst. Evol. 49(3):176-181. https://doi.org/10.1111/j.1759-6831.2011.00134.x
  58. Yuan, Q.J., B. Zhang, D. Jiang, W.J. Zhang, T.Y. Lin, N.H. Wang, S.J. Chiou and L.Q. Quang. 2015. Identification of species and materia medica within Angelica L. (Umbelliferae) based on phylogeny inferred from DNA barcodes. Mol. Ecol. Resour. 15(2):358-371. https://doi.org/10.1111/1755-0998.12296