Nucleotide Sequence Variations in a Medicinal Relative of Asparagus, Asparagus cochinchinensis (Lour.) Merrill (Asparagaceae)


To determine the eVolutionary history of Asparagus cochinchinensis (Asparagaceae), we investigated the geographic pattern of its nucleotide sequence variations in Japan, Taiwan, South Korea and China. We found 21 polymorphic nucleotide sites by sequencing the internal transcribed spacer (ITS) region, which gave rise to a total of 15 haplotypes, labeled A to O. The A-type was found only in inland China (Guizhou and Sichuan), and the other haplotypes in China extended to several lineages; therefore, A. cochinchinensis may have its origin in the interior of China. The I-type has large distribution area and it also experienced a quick expansion in relative recent years. Haplotype differentiation was observed between the eastern and western side of the Central Mountain Ridge in Taiwan. Two lineages were found in Japan, one in the Yaeyama Islands and the other in remaining areas of Japan, implying that A. cochinchinensis independently colonized in Japan at least twice.

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T. Fukuda, I. Song, T. Ito, H. Hayakawa, Y. Minamiya, A. Kanno, H. Nakayama and J. Yokoyama, "Nucleotide Sequence Variations in a Medicinal Relative of Asparagus, Asparagus cochinchinensis (Lour.) Merrill (Asparagaceae)," American Journal of Plant Sciences, Vol. 2 No. 6, 2011, pp. 765-775. doi: 10.4236/ajps.2011.26091.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] M. Nei and S. Kumar, “Molecular EVolution and Phylogenetics,” Oxford University Press, New York, 2000, pp. 3-16.
[2] J. C. Avise, J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb and N. C. Saunders, “Intraspecific Phylogeography: The Mitochondrial DNA Bridge between Population Genetics and Systematics,” Annual Review of Ecology, Evolution, and Systematics, Vol. 18, 1987, pp. 489-552.
[3] J. C. Avise, “Molecular Markers, Natural History, and Evolution,” Chapman & Hall, New York, 1994. doi:10.1007/978-1-4615-2381-9
[4] J. C. Avise, “Phylogeography: The History and Formation of Species,” Harvard University Press, Cambridge, 2000.
[5] E. Beckler and T. Holtsford, “Zea Systematics: Ribosomal ITS Evidence,” Molecular Biology and Evolution, Vol. 13, No. 4, 1996, pp. 612-622.
[6] B. A. Schaal and K. M. Olsen, “Gene Genealogies and Population Variation in Plants,” Proceedings of the National Academic of Sciences of the United States of America, Vol. 97, No. 13, 1999, pp. 7024-7029.
[7] K. M. Olsen, “Population History of Manihot esculenta (Euphorbiaceae) Inferred from Nuclear DNA Sequences,” Molecular Ecology, Vol. 11, No. 5, 2002, pp. 901-911. doi:10.1046/j.1365-294X.2002.01493.x
[8] K. M. Olsen and M. D. Purugganan, “Molecular Evidence on the Origin and Evolution of Glutinous Rice,” Genetics, Vol. 162, No. 2, 2002, pp. 941-950.
[9] K. Liu, M. M. Goodman, S. Muse, J. S. C. Smith, E. S. Buckler and J. Doebley, “Genetic Structure and Diversity among Maize Inbred Lines as Inferred from DNA Microsatellites,” Genetics, Vol. 165, No. 4, 2003, pp. 2117-2128.
[10] Y. Vigouroux, Y. Matsuoka and J. Doebley, “Directional Evolution for Microsatellite Size in Maize,” Molecular Biology and Evolution, Vol. 20, No. 9, 2003, pp. 1480-1483. doi:10.1093/molbev/msg156
[11] A. V. Harter, K. A. Gardner, D. Falush, D. L. Lentz, R. A. Bye and L. H. Rieseberg, “Origin of Extant Domesticated Sunflowers in Eastern North America,” Nature, Vol. 430, 2004, pp. 201-205. doi:10.1038/nature02710
[12] I. M. Ehrenreich and M. D. Purugganan, “The Molecular Genetic Basis of Plant Adaptation,” American Journal of Botany, Vol. 93, No. 7, 2008, pp. 953-962. doi:10.3732/ajb.93.7.953
[13] B. L. Gross and K. M. Olsen, “Genetic Perspectives on Crop Domestication,” Trends in Plant Science, Vol. 15, No. 9, 2010, pp. 529-537. doi:10.1016/j.tplants.2010.05.008
[14] S. D. Tanksley and S. R. McCouch, “Seed Banks and Molecular Maps: Unlocking Genetic Potential from the Wild,” Science, Vol. 277, No. 5329, 1997, pp. 1063-1066. doi:10.1126/science.277.5329.1063
[15] K. M. Olsen and B. A. Schaal, “Evidence on the Origin of Cassava: Phylogeography of Manihot esculenta,” Proceedings of the National Academic of Sciences of the United States of America, Vol. 96, No. 10, 1999, pp. 5586-5591. doi:10.1073/pnas.96.10.5586
[16] J. Yokoyama, T. Fukuda, A. Yokoyama and M. Maki, “The Intersectional Hybrid between Weigela hortensis and W. maximowiczii (Caprifoliaceae),” Botanical Journal of the Linnean Society, Vol. 138, No. 3, 2002, pp. 369-380. doi:10.1046/j.1095-8339.2002.00033.x
[17] T. Fukuda, J. Yokoyama and H. Tsukaya, “The Evolutionary Origin of Indeterminate Leaves in Meliaceae: Phylogenetic Relationships among Species in the Genera Chisocheton and Guarea, as Inferred from Sequences of Chloroplast DNA,” International Journal of Plant Sciences, Vol. 164, 2003, pp. 13-24. doi:10.1086/344741
[18] H. Tsukaya, T. Fukuda and J. Yokoyama, “Hybridization and Introgression between Callicarpa japonica and C. mollis (Verbenaceae) in Central Japan, as Inferred from Nuclear and Chloroplast DNA Sequences,” Molecular Ecology, Vol. 12, No. 11, 2003, pp. 3003-3011. doi:10.1046/j.1365-294X.2003.01961.x
[19] J. Yokoyama, T. Fukuda and H. Tsukaya, “Morphological and Molecular Variation of Mitchella undulata Sieblod et Zucc., with Special Reference to Systematic Treatment of the Dwarf Form from Yakushima Island,” Journal of Plant Research, Vol. 116, No. 4, 2003, pp. 309-316. doi:10.1007/s10265-003-0105-7
[20] T. Yamashiro, T. Fukuda, J. Yokoyama and M. Maki, “Molecular Phylogeny of Vincetoxicum (ApocynaceaeAsclepiadoideae) Based on the Nucleotide Sequences of cpDNA and nrDNA,” Molecular Phylogenetics and Evolution, Vol. 31, No. 2, 2004, pp. 689-700. doi:10.1016/j.ympev.2003.08.016
[21] H. Tsukaya, “Gene Flow between Impatiens radicaus and I. javensis (Balsaminaceae) in Gunung Pangorango, Central Java, Indonesia,” American Journal of Botany, Vol. 91, No. 12, 2005, pp. 2119-2123.
[22] T. Feng, S. R. Downie, Y. Yu, X. Zhang, W. Chen, X. He and S. Liu, “Molecular Systematics of Angelica and Allied Genera (Apiaceae) from the Hengduan Mountains of China Based on nrDNA ITS Sequences: Phylogenetic Affinities and Biogeographic Implications,” Journal of Plant Research, Vol. 122, No. 4, 2009, pp. 403-414. doi:10.1007/s10265-009-0238-4
[23] C. Ferris, R. P. Oliver, A. J. Davy and G. M. Hewitt, “Native Oak Chloroplasts Reveal an Ancient Divide across Europe,” Molecular Ecology, Vol. 2, No. 6, 1993, pp. 337-344. doi:10.1111/j.1365-294X.1993.tb00026.x
[24] S. Dumolin-Lapegue, M. H. Pemonge, L. Gielly, P. Taberlet and R. J. Petit, “Amplification of Oak DNA from Ancient and Modern Wood,” Molecular Ecology, Vol. 8, No. 12, 1997, pp. 2137-2140. doi:10.1046/j.1365-294x.1999.00788.x
[25] S. Dumolin-Lapegue, B. Demesure, S. Fineschi, V. L. Corre and R. J. Petit, “Phylogeographic Structure of White Oaks Throughout the European Continent,” Genetics, Vol. 146, No. 4, 1999, pp. 1475-1487.
[26] T. Fukuda, J. Yokoyama and H. Ohashi, “Phylogeny and Biogeography in Lycium (Solanaceae): Inferences from Chroloplast DNA Sequences,” Molecular Phylogenetics and Evolution, Vol. 19, No. 2, 2001, pp. 246-258. doi:10.1006/mpev.2001.0921
[27] N. Fujii, N. Tomaru, K. Okuyama, K. Koike, T. Mikami and K. Ueda, “Chloroplast DNA Phylogeography of Fagus crenata (Fagaceae) in Japan,” Plant Systematics and Evolution, Vol. 232, No. 1-2, 2002, pp. 21-33. doi:10.1007/s006060200024
[28] L. H. Bailey, “Asparagus L.,” In: L. H. Bailey, Ed., The Standard Cyclopedia of Horticulture, The Macmillan Company, New York, 1944, pp. 406-411.
[29] F. J. Chittenden, “Asparagus L.,” In; F. J. Chittenden, Ed., Dictionary of Gardening, Clarendon Press, Oxford, 1956, pp. 193-196.
[30] B. Valdes, “Asparagus L.,” In: T. G. Tutin, V. H. Heywood, N. A. Burges, D. M. Moore, D. H. Valentine, S. M. Walters and D. A. Webb, Eds., Flora Europaeana, Cambridge University Press, Cambridge, 1964, pp. 71-73.
[31] J. Ohwi, “Asparagus L.,” In: F. G. Meyer and E. H. Walker, Eds., Flora of Japan, Smithonian Institution, Washington DC, 1965.
[32] V. L. Komarov, “Asparagus L.,” In: V. L. Komarov, Ed., Flora of the USSR, Vol. IV., Israel Program for Scientific Translations, Jerusalem, 1968, pp. 325-339.
[33] R. M. T. Dahlgren, H. T. Clifford and P. F. Yeo, “Asparagus L.,” In: R. M. T. Dahlgren, H. T. Clifford and P. F. Yeo, Eds., The Families of the Monocotyledons, SpringerVerlag Berlin, Heidelberg, 1985, pp. 140-142. doi:10.1007/978-3-642-61663-1
[34] H. T. Clifford and J. G. Conran, “Asparagus L.,” In: A. S. George, Ed., Flora of Australia, Australian Government Publishing Service, Canberra, 1987, pp. 159-164.
[35] K. Kubituki and P. J. Rudall, “Asparagus L.,” In: K. Kubituki, Ed., The Families and Genera of Vascular Plants, Vol. 3. Springer-Verlag Berlin, Heidenberg, 1998, pp. 125-128.
[36] D. K. Kar and S. Sen, “Chromosome Characteristics of Asparagus-Sapogenin Yielding Plant,” Cytologia, Vol. 50, 1985, pp. 147-155. doi:10.1508/cytologia.50.147
[37] X. Chen and K. G. Tamanian, “Asparagus L.,” In: Z. Wu and P. H. Raven, Eds., Flora of China, Vol. 24, Missouri Botanical Garden Press, St. Louis, 2000, pp. 139-146.
[38] T. Fukuda, H. Ashizawa, T. Nakamura, T. Ochiai, A. Kanno, T. Kameya and J. Yokoyama, “Molecular Phylogeny of the Genus Asparagus (Asparagaceae),” Plant Species Biology, Vol. 20, No. 2, 2005, pp. 121-132. doi:10.1111/j.1442-1984.2005.00131.x
[39] A. Kanno, Y.-O. Lee and T. Kameya, “The Structure of the Chloroplast Genome in Members of the Genus Asparagus,” Theoretical and Applied Genetics, Vol. 95, No. 8, 1997, pp. 1196-1202. doi:10.1007/s001220050681
[40] T. Fukuda, I.-J. Song, T. Nakamura, M. Nakada, A. Kanno, T. Kameya, H. Yamaji, S. Terabayashi, S. Takeda, M. Aburada and J. Yokoyama, “Molecular Identification of Tiandong Derived from Asparagus cochinchinensis (Lour.) Merrill by Two Typical Deletions in cpDNA,” Natural Medicines, Vol. 59, 2005, pp. 91-94.
[41] T. J. White, T. Bruns, S. Lee and J. Taylor, “Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics,” In: M. Innis, D. Gelfand, J. Sninsky and T. J. White, Eds., PCR Protocols: A Guide to Methods and Application, Academic Press, San Diego, 1990, pp. 315-322.
[42] J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin and D. G. Higgins, “The Clustal_X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools,” Nucleic Acids Research, Vol. 25, No. 24, 1997, pp. 4876-4882. doi:10.1093/nar/25.24.4876
[43] D. L. Swofford, “PAUP*. Phylogenetic Analysis Using Parsimony (and Other Methods) Version 4.0b10,” Sinauer Associates, Sunderland, 2002,
[44] W. P. Maddison, “The Discovery and Importance of Multiple Islands of Most-Parsimonious Trees,” Systematic Zoology, Vol. 40, No. 3, 1991, pp. 315-328. doi:10.2307/2992325
[45] J. Felsenstein, “Confidence Limits on Phylogenies: An Approach Using the Bootstrap,” Evolution, Vol. 39, 1985, pp. 783-791. doi:10.2307/2408678
[46] B. G. Baldwin, M. J. Sanderson, J. M. Porter, M. F. Wojciechowski, C. S. Campbell and M. J. Donoghue, “The ITS Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny,” Annals of the Missouri Botanica Garden, Vol. 82, No. 2, 1995, pp. 247-277. doi:10.2307/2399880
[47] T. Sang, D. J. Crawford and T. F. Stuessy, “ITS Sequences and the Phylogeny of the Genus Robinsonia (Asteraceae),” Systematic Zoology, Vol. 20, No. 1, 1995, pp. 55-64.
[48] P. Taberlet, L. Gielly, G. Pautou and J. Boubet, “Universal Primers for Amplication of Three Non-Coding Regions of Chloroplast DNA,” Plant Molecular Biology, Vol. 17, No. 5, 1991, pp. 1105-1109. doi:10.1007/BF00037152
[49] T. Nishizawa and Y. Watano, “Primer Pairs Suitable for PCR-SSCP Analysis of Chloroplast DNA in Angiosperms,” Journal of Phytogeography and Taxonomy, Vol. 48, 2000, pp. 67-70.
[50] C. W. Dick, K. Abdul-Salim and E. Bermingham, “Molecular Systematic Analysis Reveals Cryptic Tertiary Diversification of a Widespread Tropical Rain Forest Tree,” The American Naturalist, Vol. 160, No. 12, 2003, pp. 691-703. doi:10.1086/379795
[51] T. Ochiai, T. Sonoda, A. Kanno and T. Kameya, “Interspecific Hybrids between Asparagus schoberioides Kunth and A. officinalis L.,” Acta Horticulturae, Vol. 589, 2002, pp. 225-229.
[52] T. Ito, T. Ochiai, T. Fukuda, H. Ashizawa, T. Sonoda, T. Kameya and A. Kanno, “Potential of Interspecific Hybrids in Asparagaceae,” Acta Horticulturae, Vol. 776, 2008, pp. 279-284.
[53] D. M. Hillis, C. Moritz, C. A. Porter and R. J. Baker, “Evidence for Biased Gene Conversion in Concerted Evolution of Ribosomal DNA,” Science, Vol. 251, No. 4991, 1991, pp. 308-310. doi:10.1126/science.1987647
[54] T. Sang, D. J. Crawford and T. F. Stuessy, “Documentation of Reticulate Evolution in Peonies (Paeonia) Using Internal Transcribed Spacer Sequences of Nuclear Ribosomal DNA: Implications for Biogeography and Concerted Evolution,” Proceedings of the National Academic of Sciences of the United States of America, Vol. 92, No. 15, 1995, pp. 6813-6817. doi:10.1073/pnas.92.15.6813
[55] J. Fuertes Aguilar, J. A. Rosselo and G. Nieto Feliner, “Nuclear Ribosomal DNA (nrDNA) Concerted Evolution in Natural and Artificial Hybrid of Armeria (Plumbaginaceae),” Molecular Ecology, Vol. 8, No. 8, 1999, pp. 1341-1346. doi:10.1046/j.1365-294X.1999.00690.x
[56] E. H. Walker, “Flora of Okinawa and the Southern Ryukyu Islands,” Smithonian Institution Press, Washington DC, 1976.

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