Molecules and Cells

, Volume 33, Issue 5, pp 497–508 | Cite as

The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); Comparative evolutionary analyses with other three asterids

  • Dong-Keun Yi
  • Hae-Lim Lee
  • Byung-Yun Sun
  • Mi Yoon Chung
  • Ki-Joong Kim
Research Article


This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5–11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7–14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.


chloroplast genome Eleutherococcus senticosus indels nucleotide diversity positional effect 


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  1. APG III. (2009). An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161, 105–121.CrossRefGoogle Scholar
  2. Bausher, M.G., Singh, N.D., Lee, S.B., Jansen, R.K., and Daniell, H. (2006). The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var ‘Ridge Pineapple’: organization and phylogenetic relationships to other angiosperms. BMC Plant Biol. 6, 21.PubMedCrossRefGoogle Scholar
  3. Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucl. Acids Res. 27, 573–580.PubMedCrossRefGoogle Scholar
  4. Bowman, C.M., and Dyer, T.A. (1986). The location and possible evolutionary significance of small dispersed repeats in Wheat ctDNA. Curr. Genet. 10, 931–941.CrossRefGoogle Scholar
  5. Bowman, C.M., Barker, R.F., and Dyer, T.A. (1988). In Wheat ctDNA, Segments of ribosomal-protein genes are dispersed repeats, probably conserved by nonreciprocal recombination. Curr. Genet. 14, 127–136.PubMedCrossRefGoogle Scholar
  6. Bryan, G.J., McNicoll, J., Ramsay, G., Meyer, R.C., and De Jong, W.S. (1999). Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants. Theor. Appl. Genet. 99, 859–867.CrossRefGoogle Scholar
  7. Cato, S.A., and Richardson, T.E. (1996). Inter- and intraspecific polymorphism at chloroplast SSR loci and the inheritance of plastids in Pinus radiata D Don. Theor. Appl. Genet. 93, 587–592.CrossRefGoogle Scholar
  8. Cheng, S., Chang, S.Y., Gravitt, P., and Respess, R. (1994). Long PCR. Nature 369, 684–685.PubMedCrossRefGoogle Scholar
  9. Chung, H.J., Jung, J.D., Park, H.W., Kim, J.H., Cha, H.W., Min, S.R., Jeong, W.J., and Liu, J.R. (2006). The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence. Plant Cell Rep. 25, 1369–1379.PubMedCrossRefGoogle Scholar
  10. Cosner, M.E., Jansen, R.K., Palmer, J.D., and Downie, S.R. (1997). The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): Multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Curr. Genet. 31, 419–429.PubMedCrossRefGoogle Scholar
  11. Cosner, M.E., Raubeson, L.A., and Jansen, R.K. (2004). Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evol. Biol. 4, 27.PubMedCrossRefGoogle Scholar
  12. Daniell, H. (1993). Foreign gene-expression in chloroplasts of higher-plants mediated by tungsten particle bombardment. Method Enzymol. 217, 536–556.CrossRefGoogle Scholar
  13. Daniell, H., Datta, R., Varma, S., Gray, S., and Lee, S.B. (1998). Containment of herbicide resistance through genetic engineering of the chloroplast genome. Nat. Biotechnol. 16, 345–348.PubMedCrossRefGoogle Scholar
  14. Daniell, H., Lee, S.B., Grevich, J., Saski, C., Quesada-Vargas, T., Guda, C., Tomkins, J., and Jansen, R.K. (2006). Complete chloro-plast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor. Appl. Genet. 112, 1503–1518.PubMedCrossRefGoogle Scholar
  15. Davydov, M., and Krikorian, A.D. (2000). Eleutherococcus senticosus (Rupr. & Maxim.). Maxim. (Araliaceae) as an adaptogen: a closer look. J. Ethnopharmacol. 72, 345–393.PubMedCrossRefGoogle Scholar
  16. Doyle, J.J., Davis, J.I., Soreng, R.J., Garvin, D., and Anderson, M.J. (1992). Chloroplast DNA inversions and the origin of the grass family (Poaceae). Proc. Natl. Acad. Sci. USA 89, 7722–7726.PubMedCrossRefGoogle Scholar
  17. Echt, C.S., DeVerno, L.L., Anzidei, M., and Vendramin, G.G. (1998). Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait. Mol. Ecol. 7, 307–316.CrossRefGoogle Scholar
  18. Edgar, R.C. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 1–19.CrossRefGoogle Scholar
  19. Funk, H.T., Berg, S., Krupinska, K., Maier, U.G., and Krause, K. (2007). Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii. BMC Plant Biol. 7, 45.PubMedCrossRefGoogle Scholar
  20. Garris, A.J., Tai, T.H., Coburn, J., Kresovich, S., and McCouch, S. (2005). Genetic structure and diversity in Oryza sativa L. Genetics 169, 1631–1638.PubMedCrossRefGoogle Scholar
  21. Guo, C.H., and Terachi, T. (2005). Variations in a hotspot region of chloroplast DNAs among common wheat and Aegilops revealed by nucleotide sequence analysis. Genes Genet. Syst. 80, 277–285.PubMedCrossRefGoogle Scholar
  22. Hachtel, W., Neuss, A., and Vomstein, J. (1991). A Chloroplast DNA inversion marks an evolutionary split in the genus Oenothera. Evolution 45, 1050–1052.CrossRefGoogle Scholar
  23. Hipkins, V.D., Marshall, K.A., Neale, D.B., Rottmann, W.H., and Strauss, S.H. (1995). A mutation hotspot in the chloroplast genome of a Conifer (Douglas-fir, Pseudotsuga) is caused by variability in the number of direct repeats derived from a partially duplicated transfer-rna gene. Curr. Genet. 27, 572–579.PubMedCrossRefGoogle Scholar
  24. Hiratsuka, J., Shimada, H., Whittier, R., Ishibashi, T., Sakamoto, M., Mori, M., Kondo, C., Honji, Y., Sun, C.R., Meng, B.Y., et al. (1989). The complete sequence of the rice (Oryza sativa) chloroplast genome — intermolecular recombination between distinct transfer-rna genes accounts for a major plastid dna inversion during the evolution of the cereals. Mol. Gen. Genet. 217, 185–194.PubMedCrossRefGoogle Scholar
  25. Hoot, S.B., and Palmer, J.D. (1994). Structural rearrangements, including parallel inversions, within the chloroplast genome of anemone and related genera. J. Mol. Evol. 38, 274–281.PubMedCrossRefGoogle Scholar
  26. Jansen, R.K., and Palmer, J.D. (1987). A chloroplast dna inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proc. Natl. Acad. Sci. USA 84, 5818–5822.PubMedCrossRefGoogle Scholar
  27. Jansen, R.K., Kaittanis, C., Saski, C., Lee, S.B., Tomkins, J., Alverson, A.J., and Daniell, H. (2006). Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol.Biol. 6, 32.PubMedCrossRefGoogle Scholar
  28. Jansen, R.K., Cai, Z., Raubeson, L.A., Daniell, H., Depamphilis, C.W., Leebens-Mack, J., Muller, K.F., Guisinger-Bellian, M., Haberle, R.C., Hansen, A.K., et al. (2007). Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc. Natl. Acad. Sci. USA 104, 19369–19374.PubMedCrossRefGoogle Scholar
  29. Jo, Y.D., Park, J., Kim, J., Song, W., Hur, C.G., Lee, Y.H., and Kang, B.C. (2011). Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome. Plant Cell Rep. 30, 217–229.PubMedCrossRefGoogle Scholar
  30. Kim, K.J., and Lee, H.L. (2004). Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 11, 247–261.PubMedCrossRefGoogle Scholar
  31. Kim, K.J., Choi, K.S., and Jansen, R.K. (2005). Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Mol. Biol. Evol. 22, 1783–1792.PubMedCrossRefGoogle Scholar
  32. Kim, J.S., Jung, J.D., Lee, J.A., Park, H.W., Oh, K.H., Jeong, W.J., Choi, D.W., Liu, J.R., and Cho, K.Y. (2006). Complete sequence and organization of the cucumber (Cucumis sativus L. cv. Baekmibaekdadagi) chloroplast genome. Plant Cell Rep. 25, 334–340.PubMedCrossRefGoogle Scholar
  33. Kim, Y.K., Park, C.W., and Kim, K.J. (2009). Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications. Mol. Cells 27, 365–381.PubMedCrossRefGoogle Scholar
  34. Kimura, Y., and Sumiyoshi, M. (2004). Effects of various Eleutherococcus senticosus cortex on swimming time, natural killer activity and corticosterone level in forced swimming stressed mice. J. Ethnopharmacol. 95, 447–453.PubMedCrossRefGoogle Scholar
  35. Kuang, D.Y., Wu, H., Wang, Y.L., Gao, L.M., Zhang, S.Z., and Lu, L. (2011). Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. Genome 54, 663–673.PubMedCrossRefGoogle Scholar
  36. Kurkin, V.A. (2003). Phenylpropanoids from medicinal plants: Distribution, classification, structural analysis, and biological activity. Chem. Nat. Compd. 39, 123–153.CrossRefGoogle Scholar
  37. Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J., and Giegerich, R. (2001). REPuter: the manifold applications of repeat analysis on a genomic scale. Nucl. Acids Res. 29, 4633–4642.PubMedCrossRefGoogle Scholar
  38. Lee, H.L., Jansen, R.K., Chumley, T.W., and Kim, K.J. (2007). Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol. Biol. Evol. 24, 1161–1180.PubMedCrossRefGoogle Scholar
  39. Librado, P., and Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452.PubMedCrossRefGoogle Scholar
  40. Lowe, T.M., and Eddy, S.R. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 25, 955–964.PubMedGoogle Scholar
  41. Maier, R.M., Neckermann, K., Igloi, G.L., and Kossel, H. (1995). Complete sequence of the maize chloroplast genome — gene content, hotspots of divergence and fine-tuning of genetic information by transcript editing. J. Mol. Biol. 251, 614–628.PubMedCrossRefGoogle Scholar
  42. Mayor, C., Brudno, M., Schwartz, J.R., Poliakov, A., Rubin, E.M., Frazer, K.A., Pachter, L.S., and Dubchak, I. (2000). VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16, 1046–1047.PubMedCrossRefGoogle Scholar
  43. McNeal, J.R., Kuehl, J.V., Boore, J.L., and de Pamphilis, C.W. (2007). Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biol. 7, 57.PubMedCrossRefGoogle Scholar
  44. Morton, B.R., and Clegg, M.T. (1993). A chloroplast dna mutational hotspot and gene conversion in a noncoding region near Rbcl in the grass family (Poaceae). Curr. Genet. 24, 357–365.PubMedCrossRefGoogle Scholar
  45. Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki, Y., Takeuchi, M., Chang, Z., et al. (1986). Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322, 572–574.CrossRefGoogle Scholar
  46. Palmer, J.D. (1986). Isolation and structural analysis of chloroplast DNA. In Methods in Enzymology, A. Weissbach, and H. Weissbach, eds. Vol. 118 (New York: Academic Press), pp. 167–186.Google Scholar
  47. Palmer, J.D. (1987). Chloroplast DNA evolution and biosystematic uses of chloroplast DNA variation. Am. Nat. 130, S6–S29.CrossRefGoogle Scholar
  48. Palmer, J.D. (1990). Contrasting modes and tempos of genome evolution in land plant organelles. Trends Genet. 6, 115–120.PubMedCrossRefGoogle Scholar
  49. Palmer, J.D. (1991). Plastid chromosomes: structure and evolution. In Cell Culture and Somatic Cell Genetics in Plants, Vol. 7A, The Molecular biology of Plastids, I.K. Vasil, and L. Bogorad, eds. (San Diego: Academic Press), pp. 5–53.Google Scholar
  50. Palmer, J.D., and Stein, D.B. (1986). Conservation of Chloroplast Genome Structure among Vascular Plants. Curr. Genet. 10, 823–833.CrossRefGoogle Scholar
  51. Plunkett, G.M., Soltis, D.E., and Soltis, P.S. (1996). Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences. Am. J. Bot. 83, 499–515.CrossRefGoogle Scholar
  52. Plunkett, G.M., Soltis, D.E., and Soltis, P.S. (1997). Clarification of the relationship between Apiaceae and Araliaceae based on matK and rbcL sequence data. Am. J. Bot. 84, 565–580.PubMedCrossRefGoogle Scholar
  53. Powell, W., Morgante, M., Andre, C., Mcnicol, J.W., Machray, G.C., Doyle, J.J., Tingey, S.V., and Rafalski, J.A. (1995). Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Curr. Biol. 5, 1023–1029.PubMedCrossRefGoogle Scholar
  54. Powell, W., Morgante, M., Mcdevitt, R., Vendramin, G.G., and Rafalski, J.A. (1995). Polymorphic simple sequence repeat regions in chloroplast genomes — applications to the populationgenetics of pines. Proc. Natl. Acad. Sci. USA 92, 7759–7763.PubMedCrossRefGoogle Scholar
  55. Provan, J., Corbett, G., Waugh, R., McNicol, J.W., Morgante, M., and Powell, W. (1996). DNA fingerprints of rice (Oryza sativa) obtained from hypervariable chloroplast simple sequence repeats. Proc. Roy. Soc. Lond. B. Bio. 263, 1275–1281.CrossRefGoogle Scholar
  56. Raubeson, L.A., and Jansen, R.K. (2005). Chloroplast genomes of plants. In diversity and evolution of plants-genotypic variation in higher plants, R. Henry, eds. (Oxfordshire, UK: CABI Publishing)., pp. 45–68.CrossRefGoogle Scholar
  57. Ruhlman, T., Lee, S.B., Jansen, R.K., Hostetler, J.B., Tallon, L.J., Town, C.D., and Daniell, H. (2006). Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7, 222.PubMedCrossRefGoogle Scholar
  58. Sambrook, J., and Russell, D. (2001). Molecular cloning: a laboratory manual. Vol. 2, 3rd edition (New York: Cold Spring Harbor), pp. 8.77–8.85.Google Scholar
  59. Samson, N., Bausher, M.G., Lee, S.B., Jansen, R.K., and Daniell, H. (2007). The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms. Plant Biotechnol. J. 5, 339–353.PubMedCrossRefGoogle Scholar
  60. Saski, C., Lee, S.B., Daniell, H., Wood, T.C., Tomkins, J., Kim, H.G., and Jansen, R.K. (2005). Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol. Biol. 59, 309–322.PubMedCrossRefGoogle Scholar
  61. Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., Zaita, N., Chunwongse, J., Obokata, J., Yamaguchishinozaki, K., et al. (1986). The complete nucleotidesequence of the tobacco chloroplast genome — its gene organization and expression. EMBO J. 5, 2043–2049.PubMedGoogle Scholar
  62. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994). Clustal-W — improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22, 4673–4680.PubMedCrossRefGoogle Scholar
  63. Wakasugi, T., Tsudzuki, J., Ito, S., Nakashima, K., Tsudzuki, T., and Sugiura, M. (1994). Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc. Natl. Acad. Sci. USA 91, 9794–9798.PubMedCrossRefGoogle Scholar
  64. Wen, J., Shi, S.H., Jansen, R.K., and Zimmer, E.A. (1998). Phylogeny and biogeography of Aralia sect. Aralia (Araliaceae). Am. J. Bot. 85, 866–875.PubMedCrossRefGoogle Scholar
  65. Wen, J., Plunkett, G.M., Mitchell, A.D., and Wagstaff, S.J. (2001). The evolution of Araliaceae: A phylogenetic analysis based on ITS sequences of nuclear ribosomal DNA. Syst. Bot. 26, 144–167.Google Scholar
  66. Wolfe, K.H., Gouy, M.L., Yang, Y.W., Sharp, P.M., and Li, W.H. (1989). Date of the monocot dicot divergence estimated from chloroplast DNA-sequence data. Proc. Natl. Acad. Sci. USA 86, 6201–6205.PubMedCrossRefGoogle Scholar
  67. Wolfe, K.H., Morden, C.W., and Palmer, J.D. (1992). Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc. Natl. Acad. Sci. USA 89, 10648–10652.PubMedCrossRefGoogle Scholar
  68. Wolfson, R., Higgins, K.G., and Sears, B.B. (1991). Evidence for replication slippage in the evolution of Oenothera chloroplast DNA. Mol. Biol. Evol. 8, 709–720.PubMedGoogle Scholar
  69. Wyman, S.K., Jansen, R.K., and Boore, J.L. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20, 3252–3255.PubMedCrossRefGoogle Scholar
  70. Xu, D.H., Abe, J., Gai, J.Y., and Shimamoto, Y. (2002). Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean. Theor. Appl. Genet. 105, 645–653.PubMedCrossRefGoogle Scholar
  71. Yang, M., Zhang, X.W., Liu, G.M., Yin, Y.X., Chen, K.F., Yun, Q.Z., Zhao, D.J., Al-Mssallem, I.S., and Yu, J. (2010). The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 5, 9.Google Scholar
  72. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res. 31, 3406–3415.PubMedCrossRefGoogle Scholar

Copyright information

© The Korean Society for Molecular and Cellular Biology and Springer Netherlands 2012

Authors and Affiliations

  • Dong-Keun Yi
    • 1
  • Hae-Lim Lee
    • 1
  • Byung-Yun Sun
    • 2
  • Mi Yoon Chung
    • 3
  • Ki-Joong Kim
    • 1
  1. 1.School of Life SciencesKorea UniversitySeoulKorea
  2. 2.Division of Biological SciencesJeonbuk National UniversityJeonjuKorea
  3. 3.Department of BiologyGyeongsang National UniversityJinjuKorea

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