DOI QR코드

DOI QR Code

Phylogenetic analysis of Viburnum (Adoxaceae) in Korea using DNA sequences

  • Received : 2018.09.01
  • Accepted : 2018.09.29
  • Published : 2018.09.30

Abstract

The nucleotide sequences of the chloroplast rbcL, matK, and psbA-trnH and nuclear internal transcribed spacer (ITS) regions were determined from all species of Viburnum in Korea with multiple accessions to reconstruct the phylogeny and to evaluate the utility of the DNA sequences as DNA barcodes. The results of phylogenetic analyses of the cpDNA and ITS data are consistent with the findings of previous studies of Viburnum. Four morphologically closely related species, V. dilatatum, V. erosum, V. japonicum, and V. wrightii, were included in a strongly supported sister clade of V. koreanum and V. opulus. Viburnum odoratissimum is suggested to be sister to the V. dilatatum/V. koreanum clade in the cpDNA data, while V. odoratissimum is a sister to V. furcatum in the ITS data. Viburnum burejaeticum and V. carlesii are strongly supported as monophyletic. Our analyses of DNA barcode regions from multiple accessions of the species of Viburnum in Korea confirm that six out of ten species in Korea can be discriminated at the species level. The V. dilatatum complex can be separated from the remaining species according to molecular data, but the resolution power to differentiate a species within the complex is weak. This study suggests that regional DNA barcodes are useful for molecular species identification in the case of Viburnum when flowering or fruiting materials are not available.

Keywords

References

  1. Ahn, D. K. 1998. Illustrated Book of Korean Medicinal Herbs. Kyohaksa, Seoul, 854 pp.
  2. Cantino, P. D., J. A. Doyle, S. W. Graham, W. S. Judd, R. G. Olmstead, D. E. Soltis, P. S. Soltis and M. J. Donoghue. 2007. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56: 822-846. https://doi.org/10.2307/25065865
  3. 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. https://doi.org/10.1073/pnas.0905845106
  4. Clement, W. L., M. Arakaki, P. W. Sweeney, E. J. Edwards and M. J. Donoghue. 2014. A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution. American Journal of Botany 101: 1029-1049. https://doi.org/10.3732/ajb.1400015
  5. Clement, W. L. and M. J. Donoghue. 2011. Dissolution of Viburnum section Megalotinus (Adoxaceae) of Southeast Asia and its implications for morphological evolution and biogeography. International Journal of Plant Sciences 172: 559-573. https://doi.org/10.1086/658927
  6. Clement, W. L. and M. J. Donoghue. 2012. Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms. BMC Evolutionary Biology 12: 73. https://doi.org/10.1186/1471-2148-12-73
  7. Cuenoud, P., V. Savolainen, L. W. Chatrou, M. Powell, R. J. Grayer and M. W. Chase. 2002. Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. American Journal of Botany 89: 132-144. https://doi.org/10.3732/ajb.89.1.132
  8. Donoghue, M. J. 1983. The phylogenetic relationships of Viburnum. Advances in Cladistics 2: 143-166.
  9. Donoghue, M. J., B. G. Baldwin, J. Li and R. C. Winkworth. 2004. Viburnum phylogeny based on chloroplast trnK intron and nuclear ribosomal ITS DNA sequences. Systematic Botany 29: 188-198. https://doi.org/10.1600/036364404772974095
  10. Donoghue, M. J., C. D. Bell and R. C. Winkworth. 2003. The evolution of reproductive characters in Dipsacales. International Journal of Plant and Science 164: S453-S464. https://doi.org/10.1086/376874
  11. 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
  12. Egolf, D. R. 1962. A cytological study of the genus Viburnum. Journal of the Arnold Arboretum 43: 132-172.
  13. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
  14. Hara, H. 1983. A Revision of Caprifoliaceae of Japan with Reference to Allied Plants in Other Districts and the Adoxaceae. Academia Scientific Books, Tokyo, 336 pp.
  15. Hebert, P. D. N., A. Cywinska, S. L. Ball and J. R. deWaard. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270: 313-321. https://doi.org/10.1098/rspb.2002.2218
  16. Hong, H.-H. and H.-T. Im. 2003. Viburnum japonicum (Caprifoliaceae): an unrecorded species in Korea. Korean Journal of Plant Taxonomy 33: 271-277. https://doi.org/10.11110/kjpt.2003.33.3.271
  17. Huelsenbeck, J. P. and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic tress. Bioinformatics 17: 754-755. https://doi.org/10.1093/bioinformatics/17.8.754
  18. Kim, H. M., S.-H. Oh, G, S. Bhandari, C.-S. Kim and C.-W. Park. 2014. DNA barcoding of Orchidaceae in Korea. Molecular Ecology Resources 14: 499-507. https://doi.org/10.1111/1755-0998.12207
  19. Kim, T. J. 2007. Viburnaceae Raf. In The Genera of Vascular Plants of Korea. Park C.-W. (ed.), Academy Publishing Co., Seoul. Pp. 944-946.
  20. Kress, W. J. and D. L. Erickson. 2007. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2: e508. https://doi.org/10.1371/journal.pone.0000508
  21. 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. https://doi.org/10.1073/pnas.0503123102
  22. Kwon, M. K., H. E. Lee, J. Y. Park and Y. S. Hahn. 2003. Antimicrobial activities of berry extract of domestic plants on 4 kinds of pathogenic microorganism. Journal of the East Asian Society of Dietary Life 13: 433-438.
  23. 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. Proceedings of the National Academy of Sciences of the United States of America 105: 2923-2928. https://doi.org/10.1073/pnas.0709936105
  24. Mabberley, D. J. 1997. The Plant-Book. 2nd ed. Cambridge University Press, Cambridge, 680 pp.
  25. Posada, D. and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818. https://doi.org/10.1093/bioinformatics/14.9.817
  26. Rehder, A. 1908. The Viburnums of eastern Asia. In Trees and Shrubs. Vol. II, Part II. Sargent, C. S. (ed.), Houghton Mifflin, Boston, MA. Pp. 105-116.
  27. Sambrook, J., E. F. Fritzsch and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Press, New York, 2100 pp.
  28. Sang, T., D. Crawford and T. Stuessy. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84: 1120-1136. https://doi.org/10.2307/2446155
  29. Soltis, P. S., D. E. Soltis and C. J. Smiley. 1992. An rbcL sequence from a Miocene Taxodium (bald cypress). Proceedings of the National Academy of Sciences of the United States of America 89: 449-451. https://doi.org/10.1073/pnas.89.1.449
  30. Son, H.-D., D.-H. Kim and H.-T. Im. 2008. A short record for the distribution of 4 rare plants. Korean Journal of Plant Taxonomy 38: 565-571. https://doi.org/10.11110/kjpt.2008.38.4.565
  31. Swofford, D. L. 2002. PAUP* Phylogenetic analysis using parsimony (* and other methods), version 4.0. Sinauer Associates, Sunderland, MA.
  32. Winkworth, R. C. and M. J. Donoghue. 2004. Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSI. Molecular Phylogenetics and Evolution 33: 109-126. https://doi.org/10.1016/j.ympev.2004.05.006
  33. Winkworth, R. C. and M. J. Donoghue. 2005. Viburnum phylogeny based on combined molecular data: implications for taxonomy and biogeography. American Journal of Botany 92: 653-666. https://doi.org/10.3732/ajb.92.4.653
  34. Xiang, X.-G., H. Hu, W. Wang and X.-H. Jin. 2011. DNA barcoding of the recently evolved genus Holcoglossum (Orchidaceae: Aeridinae): a test of DNA barcode candidates. Molecular Ecology Resources 11: 1012-1021. https://doi.org/10.1111/j.1755-0998.2011.03044.x
  35. 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
  36. Zhang, N., W. Sun and J. Yang. 2016. Chromosome counts and karyotype analysis of Viburnum taxa (Adoxaceae). Caryologia 69: 12-19. https://doi.org/10.1080/00087114.2015.1109929

Cited by

  1. A comparative morphological study of Viburnum (Adoxaceae) in Korea vol.49, pp.2, 2018, https://doi.org/10.11110/kjpt.2019.49.2.107
  2. The complete chloroplast genome sequence of Viburnum erosum (Adoxaceae) vol.4, pp.2, 2019, https://doi.org/10.1080/23802359.2019.1667919
  3. 한국산 도둑놈의갈고리족(콩과)의 DNA 바코드 및 계통학적 연구 vol.49, pp.3, 2018, https://doi.org/10.11110/kjpt.2019.49.3.224
  4. Comparative chloroplast genomics and phylogenetic analysis of the Viburnum dilatatum complex (Adoxaceae) in Korea vol.50, pp.1, 2018, https://doi.org/10.11110/kjpt.2020.50.1.8
  5. Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri vol.10, pp.3, 2018, https://doi.org/10.3390/plants10030487