Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications

Molecules and Cells

Volumn 27, Issue 3, 2009, Pages 365-381

  Kim, Young Kyu ^a   Park, Chong Wook ^b   Kim, Ki Joong ^a  

^a Korea University   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

Base substitution rate; Chloroplast genome; Endangered genus in Korea; Indel mutation; Megalreanthis; Phylogeny; Positional effect; Simple sequence repeat; Trollius

Indexed keywords

ARTICLE; CHLOROPLAST; CODON; DNA SEQUENCE; GENE FREQUENCY; GENE ORDER; INCIDENCE; INDEL MUTATION; INTRON; MEGALERANTHIS SANICULIFOLIA; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT; PLANT GENOME; RANUNCULACEAE; SIMPLE SEQUENCE REPEAT; AMINO ACID SEQUENCE; GENETICS; KOREA; MOLECULAR GENETICS; PLANT GENE; SEQUENCE ALIGNMENT;

EMBRYOPHYTA; MEGALERANTHIS; MEGALERANTHIS SANICULIFOLIA; RANUNCULACEAE; RANUNCULUS; TROLLIUS;

CHLOROPLAST DNA;

AMINO ACID SEQUENCE; BASE SEQUENCE; CHLOROPLASTS; DNA, CHLOROPLAST; GENES, PLANT; GENOME, PLANT; KOREA; MOLECULAR SEQUENCE DATA; PHYLOGENY; RANUNCULACEAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 70349305662     PISSN: 10168478     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10059-009-0047-6     Document Type: Article

References (64)

1. S.A. Cato T.E. Richardson 1996 Inter- and intra-specific polymorphism at chloroplast SSR loci and the inheritance of plastids in Pinus radiata D Don. Theor. Appl. Genet. 93 587 592 10.1007/BF00417952 1:CAS:528:DyaK28XmtF2nsbo%3D
2. M.E. Cosner R.K. Jansen J.D. Palmer S.R. Downie 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. Gennet. 31 419 429 10.1007/s002940050225 1:CAS:528:DyaK2sXjvFOkt70%3D (Pubitemid 27273691)
3. M.E. Cosner L.A. Raubeson R.K. Jansen 2004 Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes BMC Evol. Biol. 4 27 15324459 10.1186/1471-2148-4-27 1:CAS:528:DC%2BD2cXotlaksLk%3D (Pubitemid 39364124)
4. J.J. Doyle J.A. Doyle 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue Phytochem. Bull. 19 11 15
5. J.J. Doyle J.I. Davis R.J. Soreng D. Garvin M.J. Anderson 1992 Chloroplast DNA inversions and the origin of the grass family (Poaceae) Proc. Natl. Acad. Sci. USA 89 7722 7726 1502190 10.1073/pnas.89.16.7722 1:CAS:528:DyaK3sXkt1CksLw%3D
6. J.S. Farris V.A. Albert M. Kallersjo D. Lipscomb A.G. Kluge 1996 Parsimony jackknifing out performs neighbor-joining Cladistics 12 94 124
7. W. Hachtel A. Neuss J.V. Stein 1991 A chloroplast DNA inversion marks an evolutionary spilt in the genus Oenothera Evolution 45 1050 1052 10.2307/2409709
8. Hermann, R.G., Oelmuller, R., Bichler, J., Schneiderbauer, A., Steppuhn, J., Wedel, N., Tyagi, A.K., and Westhoff, P. (1991). The thylakoid membrane of higher plants: genes, their expression and interaction. In Plant Molecular Biology 2, R.G. Hermann, and B. Larkins, eds., (New York, USA: Plaenum Press), pp. 411-427.
9. D.G. Higgins J.D. Thompson T.J. Gibson 1996 Using CLUSTAL for multiple sequence alignments Methods Enzymol. 266 383 402 8743695 10.1016/S0076-6879(96) 66024-8 1:CAS:528:DyaK28Xltl2nt7w%3D (Pubitemid 26165878)
10. J. Hiratsuka H. Shimada R. Whittier T. Ishibashi M. Sakamoto M. Mori C. Kondo Y. Honji C.R. Shun B.Y. Meng, et al. 1989 The complete sequence of the rice (Oryza sativa chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals Mol. Gen. Genet. 217 185 194 2770692 10.1007/BF02464880 1:CAS:528:DyaL1MXlt1yjs7k%3D
11. S.B. Hoot 1991 Phylogeny of the Ranunculaceae based on epidermal microcharacters and macromophology Syst. Bot. 16 741 755 10.2307/2418876
12. S.B. Hoot J.D. Palmer 1994 Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera J. Mol. Evol. 38 274 281 8006994 10.1007/BF00176089 1:CAS:528:DyaK2cXitlOnsL8%3D
13. U. Jansen 1966 Die Verwandtschaftverhaltnisse innerhalb der Ranunculaceae aus serologischer Sicht Ber. Deutsch. Bot. Ges. 79 407 412
14. U. Jansen 1968 Serologische Beitrage zur Systematik der Ranunculaceae Bot. Jahrb. 88 269 310
15. R.K. Jansen J.D. Palmer 1987 A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae) Proc. Natl. Acad. Sci. USA 84 5818 5822 16593871 10.1073/pnas.84.16.5818 1:CAS:528:DyaL2sXlt1ygtbg%3D
16. R.K. Jansen Z. Cai L.A. Raubeson H. Daniell C.W. dePamphilis J.L. Mack K.F. Muller M.G. Bellian R.C. Haberle A.K. Hansen, 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 18048330 10.1073/pnas.0709121104 1:CAS:528:DC%2BD1cXitlWjtg%3D%3D
17. U. Jensen S.B. Hoot J.T. Johansson K. Kosuge 1995 Systematic and phylogeny of the Ranunculaceae, a revised family concept on the basis of molecular data Plant Syst. Evol. 9 273 280
18. J.T. Johansson R.K. Jansen 1991 Chloroplast DNA variation among the five species of Ranunculaceae: structure, sequence divergence, and phylogenetic relationships Plant Syst. Evol. 178 9 25 10.1007/BF00937979 1:CAS:528: DyaK38XisFahur0%3D
19. A. Kanno A. Hirai 1993 A transcription map of the chloroplast genome from rice (Oryza sativa) Curr. Genet. 23 166 174 8381719 10.1007/BF00352017 1:CAS:528:DyaK3sXhs1ahtLk%3D (Pubitemid 23045019)
20. M. Kim S. Lee 1987 Palynotaxonomic relationship of Megaleranthis saniculifolia Ohwi to the relative species Korean J. Plant Taxon. 17 13 20
21. K.J. Kim H.L. Lee 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 15500250 10.1093/dnares/11.4.247 1:CAS:528:DC%2BD2cXnvVWlt7c%3D (Pubitemid 40040655)
22. K.J. Kim K.S. Choi R.K. Jansen 2005 Two chloroplast DNA inversions originated simultaneously during early evolution in the sunflower family Mol. Biol. Evol. 22 1783 1792 15917497 10.1093/molbev/msi174 1:CAS:528: DC%2BD2MXosVegurw%3D (Pubitemid 41191505)
23. E.B. Knox J.D. Palmer 1999 The chloroplast genome arrangement of Lobelia thuliniana (Lobeliaceae): expansion of the inverted repeat in an ancestor of the Campanulales Plant Syst. Evol. 214 49 64 10.1007/BF00985731
24. S. Kumar K. Tamura I. Jakobsen M. Nei 2001 MEGA2: molecular evolutionary genetics analysis. ver. 2.1 Bioinformatics 17 1244 1245 11751241 10.1093/bioinformatics/17.12.1244 1:CAS:528:DC%2BD38XmtVCktQ%3D%3D
25. S. Kurtz J.V. Choudhuri E. Ohlebusch C. Schleiermacher J. Stoye R. Giegerich 2001 REPuter: the manifold applications of repeat analysis on a genomic scale Nucleic Acids Res. 29 4633 4642 11713313 10.1093/nar/29.22.4633 1:CAS:528:DC%2BD3MXptV2iu74%3D
26. S. Lee 1989 Palynological evidence for the relationships between Megaleranthis saniculifolia and Trollius species Pollen et Spores 31 173 185
27. S. Lee 1990 On the taxonomic position of Trollius chosensis Owhi (Ranunculaceae) Korean. J. Pl. Taxon. 20 1 8
28. S. Lee 1992 Palynological relationships among Calathodes and its relative genera Korean. J. Pl. Taxon 22 23 31
29. Lee, Y.N. (2007). Flora of Korea, the 2nd ed. (Seoul, Korea: Kyohaksa).
30. Y.N. Lee S.H. Yeau 1985 Taxonomic characters of Megaleranthis saniculifolia Ohwi (Ranunculaceae) Korean J. Plant Taxon. 15 127 131
31. S. Lee S. Blackmore 1992 A palynotaxonomic study of the genus Trollius Grana 31 81 100 10.1080/00173139209430728
32. H.L. Lee R.K. Jansen T.W. Chumley K.J. Kim 2007 Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions Mol. Biol. Evol. 24 1161 1180 17329229 10.1093/molbev/msm036 1:CAS:528:DC%2BD2sXmtVOis7g%3D (Pubitemid 47343642)
33. E.E. Leppik 1964 Floral evolution in Ranunculaceae Iowa State Coll. Sci. 39 1 104
34. J. Lidholm P. Gustafsson 1991 A three-step model for the rearrangement of chloroplast trnK-psbA region of the gymnosperm Pinus contorta Nucleic Acids Res. 19 2881 2887 2057349 10.1093/nar/19.11.2881 1:CAS:528:DyaK38XhtVSgtbY%3D
35. B.G. Milligan J.N. Hampton J.D. Palmer 1989 Dispersed repeats and structural reorganization in subclover chloroplast DNA Mol. Biol. Evol. 6 355 368 2615639 1:CAS:528:DyaL1MXltFSisrs%3D
36. Y. Ogihara T. Terachi T. Sasakuma 1988 Intramolecular recombination of chloroplast genome mediated by a short direct-repeat sequence in wheat species Proc. Natl. Acad. Sci. USA 85 8573 8577 3186748 10.1073/pnas.85.22.8573 1:CAS:528:DyaL1MXhvFejsg%3D%3D
37. J. Ohwi 1935 Megaleranthis, genus novum Ranunculacearum Acta Phytotax. Geobot. 4 130 131
38. J. Ohwi 1937 Symbolae ad floram Asiae orientalis 15 Acta Phytotax. Geobot. 6 145 153
39. J.D. Palmer 1990 Contrasting modes and tempos of genome evolution in land plant organelles Trends Genet. 6 115 120 2132730 10.1016/0168-9525(90)90125-P 1:CAS:528:DyaK3cXkslWqsr0%3D
40. 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, USA: Academic Press), pp. 5-53.
41. J.D. Palmer W.F. Thompson 1981 Rearrangements in the chloroplast genomes of mung bean and pea Proc. Natl. Acad. Sci. USA 78 5533 5537 16593087 10.1073/pnas.78.9.5533 1:CAS:528:DyaL3MXlvVCjtrc%3D
42. J.D. Palmer J.M. Nugent L.A. Herbon 1987 Unusual structure of geranium chloroplast DNA: A triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families Proc. Natl. Acad. Sci. USA 84 769 773 16593810 10.1073/pnas.84.3.769 1:CAS:528:DyaL2sXhtlaku7k%3D
43. J.D. Palmer B. Osorio J. Aldrich W.F. Thompson 1987 Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements Curr. Genet. 11 275 286 10.1007/BF00355401 1:CAS:528:DyaL2sXhsFSmtb8%3D
44. Park, C.-W., Yeau, S.H., Chang, C.S., Lee, H.W., and Sun, B.Y. (2007). Ranunculaceae. In The Genera of Vascular Plants of Korea. C.-W. Park, ed. (Seoul, Korea: Academy Publ. Co.), pp. 165-205.
45. W. Powell M. Morgante C. Andre M. Hanafey J. Vogel S. Tingey A. Rafalski 1996 The utility of RFLP, RAPD, AFLP and SSRP (microsatellite) markers for germplasm analysis? Mol. Breed. 2 225 238 10.1007/BF00564200 1:CAS:528:DyaK28XntlGrtLk%3D
46. J. Provan G. Corbett R. Waugh J.W. McNicol M. Morgante W. Powell 1996 DNA fingerprints of rice (Oryza sativa) obtained from hypervariable simple sequence repeats Proc. R. Soc. London Ser. B 263 1275 1281 10.1098/rspb.1996.0187 1:CAS:528:DyaK28XntVeit7w%3D (Pubitemid 26370874)
47. 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, ed. (Oxfordshire, United Kingdom: CABI Publishing), pp.45-68.
48. L.A. Raubeson R. Peery T.W. Chumley C. Dziubek H.M. Fourcade J.L. Boore R.K. Jansen 2007 Comparative chloroplast genomics analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus BMC Genomics 8 174 17573971 10.1186/1471-2164-8-174 1:CAS:528:DC%2BD2sXot1Slt7w%3D (Pubitemid 47090617)
49. K.E. Ro C.S. Keener B.A. Mcpheron 1997 Molecular phylogenetic study of the Ranunculaceae: utility of the nuclear 26S Ribosomal DNA in inferring intrafamilial relationships Mol. Phylog. Evol. 8 117 127 10.1006/mpev.1997.0413 1:CAS:528:DyaK2sXmsVamurs%3D (Pubitemid 127347510)
50. N. Saitou M. Nei 1985 The neighbor-joining method: A new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 406 425
51. Sambrook, J., Fritsch, E.F., and Maniatis, R. (1989). Molecular Cloning, a laboratory manual, the 2nd ed. (New York: USA, Cold Spring Harbor Lab Press).
52. T. Santisuk 1979 A palynological study of the tribe Ranunculeae Opera Bot. 48 1 74
53. C. Saski S.B. Lee H. Daniell T.C. Wood J. Tomkins H.G. Kim R.K. Jansen 2005 Complete chloroplast genome sequences of Glycine max and comparative analyses with other legume genomes Plant Mol. Biol. 59 309 322 16247559 10.1007/s11103-005-8882-0 1:CAS:528:DC%2BD2MXhtFCrtLfP (Pubitemid 41500491)
54. K. Shinozaki M. Ohem M. Tanaka T. Wakasugi N. Hayashida T. Matsubayashi N. Zaita J. Chunwongse J. Obokata K.Y. Shinozaki, et al. 1986 The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression EMBO J. 5 2043 2049 16453699 1:CAS:528:DyaL28Xls1Kjt7o%3D
55. K. Shinozaki N. Hayashida M. Sugiura 1988 Nicotiana chloroplast genes for components of the photosynthetic apparatus Photosyn. Res. 18 7 31 10.1007/BF00042978 1:CAS:528:DyaL1cXmtVGktbw%3D
56. S.H. Strauss J.D. Palmer G.T. Howe A.H. Doerksen 1998 Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged Proc. Natl. Acad. Sci. USA 85 3898 3902 10.1073/pnas.85.11.3898
57. Swofford, D.L. (2002). PAUP: phylogenetic analysis using parsimony and other methods, ver. 4.0. (Sunderland, USA, Sinauer Assoc.).
58. M. Tamura 1966 Morphology, ecology, and phylogeny of the Ranunculaceae VI Sci. Rep. Osaka Univ. 15 13 35
59. M. Tarnura 1990 A new classification of the family Ranunculaceae 1 Acta. Phytotax. Geobot. 41 93 101
60. Tamura, M. (1993). Ranunculaceae. In The Families and Genera of Vascular Plants: Flowering Plants-Dicotyledons, Vol. II. K. Kubitski, J. G. Rohwer, and V. Bittrich, eds. (Berlin: Germany, Springer Verlag), pp. 563-583.
61. M. Tamura 1995 Phylogeny and classification of the Ranunculaceae Plant Syst. Evol. 9 201 206
62. K.H. Wolfe M. Gouy Y.W. Yang P. Sharp W.H. Li 1989 Date of the monocot-dicot divergence estimated from chloro-plast DNA sequence data Proc. Natl. Acad. Sci. USA 86 6201 6205 2762323 10.1073/pnas.86.16.6201 1:CAS:528:DyaL1MXltlSqsLY%3D
63. S.K. Wyman R.K. Jansen J.L. Boore 2004 Automatic annotation of organellar genomes with DOGMA Bioinformatics 20 3252 3255 15180927 10.1093/bioinformatics/ bth352 1:CAS:528:DC%2BD2cXhtVSrur%2FJ (Pubitemid 39619219)
64. Q. Yuan Q.E. Yang 2006 Tribal relationships of Beesia, Eranthis and seven other genera of Ranunculaceae: evidence from cytological characters Bot. J. Linn. Soc. 150 267 289 10.1111/j.1095-8339.2006.00477.x