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

Molecules and Cells

Volumn 33, Issue 5, 2012, Pages 497-508

  Yi, Dong Keun ^a   Lee, Hae Lim ^a   Sun, Byung Yun ^b   Chung, Mi Yoon ^c   Kim, Ki Joong ^a  

^a Korea University   (South Korea)

^b Chonbuk National University   (South Korea)

^c Gyeongsang National University   (South Korea)

Author keywords

Chloroplast genome; Eleutherococcus senticosus; Indels; Nucleotide diversity; Positional effect

Indexed keywords

CHLOROPLAST DNA;

ARTICLE; ASTERID; CODON; COMPARATIVE STUDY; DNA POLYMORPHISM; DNA SEQUENCE; DNA STRUCTURE; ELEUTHEROCOCCUS SENTICOSUS; GENE DOSAGE; GENE ORDER; GENETIC TRANSCRIPTION; INTRON; INVERTED REPEAT; NONHUMAN; SIMPLE SEQUENCE REPEAT;

BASE SEQUENCE; CHLOROPLASTS; CODON; DNA, CHLOROPLAST; ELEUTHEROCOCCUS; EVOLUTION, MOLECULAR; GENE ORDER; GENES, PLANT; GENOME, CHLOROPLAST; GENOME, PLANT; INTRONS; MOLECULAR SEQUENCE DATA; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

ARALIACEAE; ASTERIDS; CODON (ANGIOSPERM); DAUCUS; ELEUTHEROCOCCUS; ELEUTHEROCOCCUS SENTICOSUS; EMBRYOPHYTA; PANAX;

EID: 84863425048     PISSN: 10168478     EISSN: 02191032     Source Type: Journal    
DOI: 10.1007/s10059-012-2281-6     Document Type: Article

References (72)

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.
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.
3. Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucl. Acids Res. 27, 573-580. (Pubitemid 29210025)
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.
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.
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. (Pubitemid 29464034)
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. (Pubitemid 26351058)
8. Cheng, S., Chang, S.Y., Gravitt, P., and Respess, R. (1994). Long PCR. Nature 369, 684-685. (Pubitemid 24199477)
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 chloro-plast 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. (Pubitemid 44786619)
10. Cosner, M.E., Jansen, R.K., Palmer, J.D., and Downie, S.R. (1997). The highly rearranged chloroplast genome of Trachelium cae-ruleum (Campanulaceae): Multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Curr. Genet. 31, 419-429. (Pubitemid 27273691)
11. Cosner, M.E., Raubeson, L.A., and Jansen, R.K. (2004). Chloro-plast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evol. Biol. 4, 27.
12. Daniell, H. (1993). Foreign gene-expression in chloroplasts of higher-plants mediated by tungsten particle bombardment. Method En-zymol. 217, 536-556. (Pubitemid 23173396)
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. (Pubitemid 28164653)
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.
15. Davydov, M., and Krikorian, A.D. (2000). Eleutherococcus sentico-sus (Rupr. & Maxim.). Maxim. (Araliaceae) as an adaptogen: a closer look. J. Ethnopharmacol. 72, 345-393.
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.
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.
18. Edgar, R.C. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 1-19.
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.
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. (Pubitemid 40547470)
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. (Pubitemid 41598021)
22. Hachtel, W., Neuss, A., and Vomstein, J. (1991). A Chloroplast DNA inversion marks an evolutionary split in the genus Oeno-thera. Evolution 45, 1050-1052.
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.
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 trans-fer-rna genes accounts for a major plastid dna inversion during the evolution of the cereals. Mol. Gen. Genet. 217, 185-194.
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. (Pubitemid 24076866)
26. Jansen, R.K., and Palmer, J.D. (1987). A chloroplast dna inversion marks an ancient evolutionary split in the sunflower family (As-teraceae). Proc. Natl. Acad. Sci. USA 84, 5818-5822.
27. Jansen, R.K., Kaittanis, C., Saski, C., Lee, S.B., Tomkins, J., Alver-son, 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.
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.
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.
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.
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. (Pubitemid 41191505)
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.
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.
34. Kimura, Y., and Sumiyoshi, M. (2004). Effects of various Eleuthero-coccus senticosus cortex on swimming time, natural killer activity and corticosterone level in forced swimming stressed mice. J. Ethnopharmacol. 95, 447-453. (Pubitemid 39422707)
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.
36. Kurkin, V.A. (2003). Phenylpropanoids from medicinal plants: Distribution, classification, structural analysis, and biological activity. Chem. Nat. Compd. 39, 123-153.
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. (Pubitemid 33095024)
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. (Pubitemid 47343642)
39. Librado, P., and Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452.
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. (Pubitemid 27298263)
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.
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. (Pubitemid 32051021)
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.
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. (Pubitemid 23317042)
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. (Pubitemid 16049213)
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.
47. Palmer, J.D. (1987). Chloroplast DNA evolution and biosystematic uses of chloroplast DNA variation. Am. Nat. 130, S6-S29.
48. Palmer, J.D. (1990). Contrasting modes and tempos of genome evolution in land plant organelles. Trends Genet. 6, 115-120.
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.
50. Palmer, J.D., and Stein, D.B. (1986). Conservation of Chloroplast Genome Structure among Vascular Plants. Curr. Genet. 10, 823-833.
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. (Pubitemid 126514368)
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. (Pubitemid 27320179)
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.
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 population-genetics of pines. Proc. Natl. Acad. Sci. USA 92, 7759-7763.
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. (Pubitemid 26370874)
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.
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.
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.
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 angio-sperms. Plant Biotechnol. J. 5, 339-353.
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. (Pubitemid 41500491)
61. Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., Zaita, N., Chunwongse, J., Obokata, J., Ya-maguchishinozaki, K., et al. (1986). The complete nucleotide-sequence of the tobacco chloroplast genome-its gene organization and expression. EMBO J. 5, 2043-2049.
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. (Pubitemid 24354800)
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. (Pubitemid 24311894)
64. Wen, J., Shi, S.H., Jansen, R.K., and Zimmer, E.A. (1998). Phylog-eny and biogeography of Aralia sect. Aralia (Araliaceae). Am. J. Bot. 85, 866-875.
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. (Pubitemid 32219360)
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.
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.
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. (Pubitemid 21895923)
69. Wyman, S.K., Jansen, R.K., and Boore, J.L. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20, 3252-3255. (Pubitemid 39619219)
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. (Pubitemid 36065021)
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.
72. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res. 31, 3406-3415. (Pubitemid 37442169)