DOI QR코드

DOI QR Code

DNA barcode and phylogenetic study of the tribe Desmodieae (Fabaceae) in Korea

한국산 도둑놈의갈고리족(콩과)의 DNA 바코드 및 계통학적 연구

  • Received : 2019.08.12
  • Accepted : 2019.09.26
  • Published : 2019.09.30

Abstract

Species identification for the Korean tribe Desmodieae was conducted using the DNA barcoding genes rbcL, matK (from chloroplast DNA) and ITS (from nuclear ribosomal DNA). A total of 25 taxa (n = 75) in five genera were sequenced, and neighbor-joining trees were constructed using different combinations of DNA barcodes. When comparing these phylogenetic trees, a tree with all loci combined (rbcL + matK + ITS) showed the highest rate of identification success (72%). On this tree, two subtribes and five genera within the tribe were supported as monophyletic. In the Desmodiinae clade, Desmodium and Hylodesmum were more closely related to each other than to Ohwia. In the Hylodesmum clade, H. oldhamii was found to be a sister to H. podocarpum complex, and all taxa within the complex were identified successfully. Subsp. fallax, regarded as a variety of subsp. oxyphyllum, is closely clustered with subsp. podocarpum. Although var. mandshuricum has been regarded as a synonym of var. oxyphyllum, this taxon is supported as a distinct variety. For the Lespedezinae clade, all species of Kummerowia were monophyletic, while nine of 16 Lespedeza taxa were identified successfully. In particular, the resolution of Macrolespedeza (28.5%) was lower than that of Junceae (77.8%). Among the Lespedeza taxa, L. cuneata was distinguishable from L. lichiyuniae, despite morphological similarities. It has been suggested that both L. maritima and L. inschanica are hybrids. The former is thought to be an independent species. While it is difficult to determine whether the latter originated via hybridization, this study showed that it is closely related to L. juncea.

본 연구에서는 DNA 바코드, 즉 엽록체 DNA의 rbcL, matK와 핵 리보솜 DNA의 ITS 염기서열을 이용하여 한국산 도둑놈의갈고리족 식물들의 종 식별을 실시하였다. 총 5개속 25분류군(총 75개체)의 식물에 대한 염기서열이 밝혀졌고, DNA 바코드 구간 조합에 따라 neighbor-joining 계통수들이 작성되었다. 그 결과, 종 식별률은 DNA 바코드 3개의 구간을 모두 사용하였을 때 가장 높게 나타났다(72%). rbcL+matK+ITS 계통수에서 본 족의 두 개의 아족과 다섯 속들은 단계통군으로 유집되었다. 도둑놈의갈고리아족군에서 도둑놈의 갈고리속과 갈고리속이 된장풀속보다 더 가깝게 묶였다. 갈고리속군에서 큰도둑놈의갈고리는 개도둑놈의갈고리 복합체의 자매군으로 형성되었고, 개도둑놈의갈고리의 종내분류군들은 각각 단계통을 형성하였다. 특히 형태적 변이로 인해 도둑놈의갈고리의 변종 또는 개도둑놈의갈고리와의 중간형으로 인식된 바 있는 긴도둑놈의갈고리는 개도둑놈의갈고리와 가장 가깝게 묶였다. 한편 도둑놈의갈고리의 변종이나 이명으로 인식되어온 애기도둑놈의갈고리는 변종으로 판단되었다. 싸리아족군의 경우, 매듭풀속 분류군들은 계통수상에서 각각 단계통으로 지지되었으나, 싸리속의 식물 16분류군 중 9분류군만 종식별이 가능하였다. 특히 싸리속내 땅비수리절보다 싸리절에서 낮은 종판별 해상능이 나타났다(싸리절=28.5%, 비수리절=77.8%). 싸리속 식물 중에 비수리는 계통수상에서 형태적으로 유사한 자주비수리와 확연히 구분되었다. 잡종으로도 인식된 바 있는 해변싸리와 청비수리 중, 해변싸리는 독립종으로 판단되었다. 반면 청비수리는 잡종 여부를 판단할 수는 없었지만, 땅비수리와 근연 관계에 있는 것으로 사료된다.

Keywords

References

  1. Akiyama, S. 1988. A revision of the genus Lespedeza section Macrolespedeza (Leguminosae). The University Museum, The University of Tokyo, Bulletin 33: 1-170.
  2. CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 106: 12794-12797.
  3. Choi, B.-H. 1991. Morphological variation and taxonomy of Desmodium podocarpium (Leguminosae) in southern Korea. Korean Journal of Plant Taxonomy 21: 55-69. (in Korean) https://doi.org/10.11110/kjpt.1991.21.1.055
  4. Choi, B. H. 2007. Lespedeza Michx. In The Genera of Vascular Plants of Korea. Park, C.-W. (ed.), Academy Publishing Co., Seoul. Pp. 614-618.
  5. 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 Journal of Plant Taxonomy 48: 206-217. https://doi.org/10.11110/kjpt.2018.48.3.206
  6. Chung, K.-A. and M.-J. Cheong. 2016. Effects of Lespedeza Caneata ethanol extract on the liver, kidneys of lead administered mice. Journal of the Korea Academia-Industrial cooperation Society 17: 207-214. (in Korean) https://doi.org/10.5762/KAIS.2016.17.6.207
  7. Dong, W., J. Liu, J. Yu, L. Wang and S. Zhou. 2012. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE 7: e35071. https://doi.org/10.1371/journal.pone.0035071
  8. Dong, W., C. Xu, C. Li, J. Sun, Y. Zuo, S. Shi, T. Cheng, J. Guo and S. Zhou. 2015. ycf1, the most promising plastid DNA barcode of land plants. Scientific Reports 5: 8348. https://doi.org/10.1038/srep08348
  9. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797. https://doi.org/10.1093/nar/gkh340
  10. Edwards, D., A. Horn, D. Taylor, V. Savolainen and J. A. Hawkins. 2008. DNA barcoding of a large genus, Aspalathus L. (Fabaceae). Taxon 57: 1317-1327. https://doi.org/10.1002/tax.574021
  11. Eun, J. S. 2011. Effect of Lespedeza cuneata G. Don on the activity of murine immune cells. Korean Journal of Oriental Physiology Pathology 25: 837-842. (in Korean)
  12. Gao, T., H. Yao, J. Song, C. Liu, Y. Zhu, X. Ma, X. Pang, H. Xu and S. Chen. 2010. Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. Journal of Ethnopharmacology 130: 116-121. https://doi.org/10.1016/j.jep.2010.04.026
  13. Han, J. E. and B.-H. Choi. 2008. Two naturalized plants of Lespedeza (Leguminosae) in Korea: L. lichiyuniae & L. davidii. Korean Journal of Plant Taxonomy 38: 547-555. (in Korean) https://doi.org/10.11110/kjpt.2008.38.4.547
  14. Han, J. E., K.-H. Chung, T. Nemoto and B.-H. Choi. 2010. Phylogenetic analysis of eastern Asian and eastern North American disjunct Lespedeza (Fabaceae) inferred from nuclear ribosomal ITS and plastid region sequences. Botanical Journal of the Linnean Society 164: 221-235. https://doi.org/10.1111/j.1095-8339.2010.01084.x
  15. Hasebe, M., T. Omori, M. Nakazawa, T. Sano, M. Kato and K. Iwatsuki. 1994. rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns. Proceedings of the National Academy of Sciences of the United States of America 91: 5730-5734.
  16. Hatusima, S. 1967. Lespedeza: sects. Macrolespedeza and Heterolespedeza from Japan, Corea and Formosa. Memoirs of the Faculty of Agriculture, Kagoshima University 6: 1-17.
  17. Hebert, P. D. N., A. Cywinska, S. L. Ball and J. R. deWaard. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B Biological Sciences 270: 313-321.
  18. Hollingsworth, P. M., S. W. Graham and D. P. Little. 2011. Choosing and using a plant DNA barcode. PLoS ONE 6: e19254. https://doi.org/10.1371/journal.pone.0019254
  19. Huang, P. H. and H. Ohashi. 2010. Desmodium Desvaux. In Flora of China. Vol. 10. Wu, Z. Y., P. H. Raven and D. Y. Hong (eds.), Science Press, Beijing and Missouri Botanical Garden Press, St. Louis, MO. Pp. 268-278.
  20. Huang, P. H., H. Ohashi and T. Nemoto. 2010. Lespedeza Michaux. In Flora of China. Vol. 10. Wu, Z. Y., P. H. Raven and D. Y. Hong (eds.), Science Press, Beijing and Missouri Botanical Garden Press, St. Louis, MO. Pp. 302-311.
  21. Jabbour, F., M. Gaudeul, J. Lambourdière, G. Ramstein, A. Hassanin, J.-N. Labat and C. Sarthou. 2018. Phylogeny, biogeography and character evolution in the tribe Desmodieae (Fabaceae: Papilionoideae), with special emphasis on the New Caledonian endemic genera. Molecular Phylogenetics and Evolution 118: 108-121. https://doi.org/10.1016/j.ympev.2017.09.017
  22. Kajita, T. and H. Ohashi. 1994. Chloroplast DNA variation in Desmodium subgenus Podocarpium (Leguminosae): infrageneric phylogeny and infraspecific variations. Journal of Plant Research 107: 349-354. https://doi.org/10.1007/BF02344263
  23. Kajita, T., H. Ohashi, Y. Tateishi, C. D. Bailey and J. J. Doyle. 2001. rbcL and legume phylogeny, with particular reference to Phaseoleae, Millettieae, and allies. Systematic Botany 26: 515-536.
  24. Kim, S. M., K. Kang, E. H. Jho, Y.-J. Jung, C. W. Nho, B.-H. Um and C.-H. Pan. 2011. Hepatoprotective effect of flavonoid glycosides from Lespedeza cuneata against oxidative stress induced by tert?butyl hyperoxide. Phytotherapy Research 25: 1011-1017. https://doi.org/10.1002/ptr.3387
  25. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120. https://doi.org/10.1007/BF01731581
  26. Kress, W. J., K. J. Wurdack, E. A. Zimmer, L. A. Weigt and D. H. Janzen. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 102: 8369-8374.
  27. Kress, W. J. and D. L. Erickson. 2008. DNA barcodes: genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences of the United States of America 105: 2761-2762.
  28. Lee, J.-Y., M. J. Kim, C.-K. Oh and B.-H. Choi. 2012. First record of Hylodesmum laxum (Fabaceae) from Korea. Korean Journal of Plant Taxonomy 42: 207-210. https://doi.org/10.11110/kjpt.2012.42.3.207
  29. Legume Phylogeny Working Group. 2013. Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species-rich clades. Taxon 62: 217-248. https://doi.org/10.12705/622.8
  30. Legume Phylogeny Working Group. 2017. A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny. Taxon 66: 44-77. https://doi.org/10.12705/661.3
  31. Lee, T. B. 1965. The Lespedeza of Korea (1). Bulletin of the Seoul National University Forests 2: 1-43.
  32. Lee, T. B. 1980. Illustrated Flora of Korea. Hyangmunsa, Seoul. Pp. 468-472.
  33. Li, H.-C., X.-L. Zhao, X.-F. Gao and B. Xu. 2019. Molecular phylogeny of the genus Hylodesmum (Fabaceae). Phytotaxa 403: 221-229. https://doi.org/10.11646/phytotaxa.403.3.6
  34. Meusnier, I., G. A. C. Singer, J.-F. Landry, D. A. Hickey, P. D. N. Hebert and M. Hajibabaei. 2008. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9: 214. https://doi.org/10.1186/1471-2164-9-214
  35. Meyer, C. P. and G. Paulay. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3: e422. https://doi.org/10.1371/journal.pbio.0030422
  36. Nakai, T. 1927. Lespedeza of Japan and Korea. The Forestal Experiment Station of Government General of Chosen 6: 1-101.
  37. Nemoto, T., J. Yokoyama, T. Fukuda, Y. Iokawa and H. Ohashi. 2010. Phylogeny of Lespedeza (Leguminosae) based on chloroplast trnL-trnF sequences. Journal of Japanese Botany 85: 213-229.
  38. Ohashi, H. 1973. The Asiatic species of Desmodium and its allied genera (Leguminosae). Ginkgoana 1: 142-155.
  39. Ohashi, H. 1999. The genera, tribes and subfamilies of Japanese Leguminosae. The Science Reports of the Tohoku University, 4th Series, Biology 40: 187-268.
  40. Ohashi, H. 2005. Desmodieae. In Legumes of the World. Lewis, G., B. Schrire, B. Mackinder and M. Lock (eds.), Royal Botanic Gardens, Kew. Pp. 432-445.
  41. Ohashi, H., R. H. Polhill and B. G. Schubert. 1981. Desmodieae. In Advances in Legume Systematics. Part 1. Polhill, R. M. and P. H. Raven (eds.), Royal Botanic Gardens, Kew. Pp. 292-300.
  42. Ohashi, H. and R. R. Mill. 2000. Hylodesmum, a new name for Podocarpium (Leguminosae). Edinburgh Journal of Botany 57: 171-188. https://doi.org/10.1017/S0960428600000123
  43. Ohashi, H. and T. Nemoto. 2014. A new system of Lespedeza (Leguminosae tribe Desmodieae). Journal of Japanese Botany 89: 1-11.
  44. Ohashi, H. and K. Ohashi. 2012. Ototropis, a genus separated from Desmodium (Leguminosae). Journal of Japanese Botany 87: 108-118.
  45. Ohashi, H. and K. Ohashi. 2018a. Grona, a genus separated from Desmodium (Leguminosae tribe Desmodieae). Journal of Japanese Botany 93: 104-120.
  46. Ohashi, H. and K. Ohashi. 2018b. Sohmaea, a new genus of Leguminosae tribe Desmodieae. Journal of Japanese Botany 93: 104-120.
  47. Ohashi, K., H. Ohashi, T. Nemoto, T. Ikeda, H. Izumi, H. Kobayashi, H. Muragaki, K. Nata, N. Sato and M. Suzuki. 2018a. Phylogenetic analyses for a new classification of the Desmodium group of Leguminosae tribe Desmodieae. Journal of Japanese Botany 93: 165-189.
  48. Ohashi, K., H. Ohashi, T. Nemoto, C. Abe, H. Kotani, K. Nata, H. Ohtake and K. Yamamoto. 2018b. Phylogenetic analyses for classification of the Desmodium group of Leguminosae tribe Desmodieae 2. Two new genera separated from Desmodium and two new combinations in Grona and Sohmaea. Journal of Japanese Botany 93: 293-306.
  49. Purty, R. S. and S. Chatterjee. 2016. DNA barcoding: an effective technique in molecular taxonomy. Austin Journal of Biotechnology & Bioengineering 3: 1059.
  50. Renner, S. S. 1999. Circumscription and phylogeny of the Laurales: evidence from molecular and morphological data. American Journal of Botany 86: 1301-1315. https://doi.org/10.2307/2656778
  51. Riahi, M., S. Zarre, A. A. Maassoumi, S. K. Osaloo and M. F. Wojciechowski. 2011. Towards a phylogeny for Astragalus section Caprini (Fabaceae) and its allies based on nuclear and plastid DNA sequences. Plant Systematics and Evolution 293: 119. https://doi.org/10.1007/s00606-011-0417-3
  52. Salazar, G. A., M. W. Chase, M. A. Soto Arenas and M. Ingrouille. 2003. Phylogenetics of Cranichideae with emphasis on Spiranthinae (Orchidaceae, Orchidoideae): evidence from plastid and nuclear DNA sequences. American Journal of Botany 90: 777-795. https://doi.org/10.3732/ajb.90.5.777
  53. Schindler, A. K. 1916. Desmodiinae novae. Botanische Jahrbücher fur Systematik, Pflanzengeschichte und Pflanzengeographie 54: 51-68.
  54. Swofford, D. L. 2002. PAUP 4.0b10: Phylogenetic analysis using parsimony. Sinauer Associates, Sunderland, MA.
  55. Vassou, S. L., G. Kusuma and M. Parani. 2015. DNA barcoding for species identification from dried and powdered plant parts: a case study with authentication of the raw drug market samples of Sida cordifolia. Gene 559: 86-93. https://doi.org/10.1016/j.gene.2015.01.025
  56. White, T. J., T. Bruns, S. Lee and J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications. Innis, M. A., D. H. Gelfand, J. J. Sninsky and T. J. White (eds.). Academic Press, New York, Pp. 315-322.
  57. Wojciechowski, M. F., M. Lavin and M. J. Sanderson. 2004. A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well?supported subclades within the family. American Journal of Botany 91: 1846-1862. https://doi.org/10.3732/ajb.91.11.1846
  58. Wolfe, K. H., W. H. Li and P. M. Sharp. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences of the United States of America 84: 9054-9058.
  59. Xu, B., N. Wu, X.-F. Gao and L.-B. Zhang. 2012. Analysis of DNA sequences of six chloroplast and nuclear genes suggests incongruence, introgression, and incomplete lineage sorting in the evolution of Lespedeza (Fabaceae). Molecular Phylogenetics and Evolution 62: 346-358. https://doi.org/10.1016/j.ympev.2011.10.007
  60. Xu, B., X.-M. Zeng, X.-F. Gao, D.-P. Jin and L.-B. Zhang. 2017. ITS non-concerted evolution and rampant hybridization in the legume genus Lespedeza (Fabaceae). Scientific Reports 7: 40057. https://doi.org/10.1038/srep40057
  61. Youm, J. W., S.-W. Han, S. W. Seo, C. U. Lim and S.-H. Oh. 2016. DNA barcoding of Schisandraceae in Korea. Korean Journal of Plant Taxonomy 46: 273-282. https://doi.org/10.11110/kjpt.2016.46.3.273