Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae)

Molecular Phylogenetics and Evolution

Volumn 45, Issue 2, 2007, Pages 547-563

  Hansen, Debra R ^a   Dastidar, Sayantani G ^a   Cai, Zhengqiu ^a   Penaflor, Cynthia ^b   Kuehl, Jennifer V ^c   Boore, Jeffrey L ^c   Jansen, Robert K ^a  

^a The University of Texas at Austin   (United States)

^b BRIGHAM YOUNG UNIVERSITY   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Austrobaileyales; Basal angiosperm phylogeny; Chloranthales; Chloroplast genome evolution; Inverted repeat

Indexed keywords

PLANT DNA;

ANGIOSPERM; ARTICLE; BIOLOGICAL MODEL; BUXUS; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; GENOME; ILLICIUM; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; PHYLOGENY; SPECIES DIFFERENTIATION; YAM;

ANGIOSPERMS; BUXUS; DIOSCOREA; DNA, PLANT; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENOME, CHLOROPLAST; ILLICIUM; MODELS, BIOLOGICAL; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TERMINAL REPEAT SEQUENCES;

ACORUS; AMBORELLA; AUSTROBAILEYALES; BUXACEAE; BUXUS; CHLORANTHACEAE; CHLORANTHALES; CHLORANTHUS; CONIFEROPHYTA; DIOSCOREA; DIOSCOREA ALATA; DIOSCOREACEAE; DRIMYS; EMBRYOPHYTA; ILLICIUM; LILIOPSIDA; MAGNOLIIDS; MAGNOLIOPHYTA; MARCHANTIOPHYTA; NUPHAR; NYMPHAEALES; POPULUS; SCHISANDRACEAE;

EID: 35148887716     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.06.004     Document Type: Article

References (108)

1. Aii J., Kishima Y., Mikami T., and Adachi T. Expansion of the IR in the chloroplast genomes of buckwheat species is due to incorporation of an SSC sequence that could be mediated by an inversion. Curr. Genet. 31 (1997) 276-279
2. Aoki S., Uehara K., Imafuku M., Hasebe M., and Ito M. Phylogeny and divergence of basal angiosperms inferred from APETALA3- and PISTILLATA-like MADS-box genes. J. Plant Res. 117 (2004) 229-244
3. Asano T., Tsudzuki T., Takahashi S., Shimada H., and Kadowaki K. Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res. 11 (2004) 93-99
4. Barkman T.J., Chenery G., McNeal J.R., Lyons-Weiler J., Ellisens W.J., Moore G., Wolfe A.D., and dePamphilis C.W. Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. Proc. Natl. Acad. Sci. USA 97 (2000) 13166-13171
5. Bausher M.G., Singh N.D., Lee S.-B., Jansen R.K., and Daniell H. The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var. 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms. BMC Plant Biol. 6 (2006) 21
6. Bömmer D., Haberhausen G., and Zetsche K. A large deletion in the plastid DNA of the holoparasitic flowering plant Cuscuta reflexa concerning two ribosomal proteins (rpl2, rpl23), one transfer RNA (trnI) and an ORF2280 homologue. Curr. Genet. 24 (1992) 171-176
7. Borsch T., Hilu K.W., Quandt D., Wilde V., Neinhuis C., and Barthlott W. Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J. Evol. Biol. 16 (2003) 558-576
8. Bremer B., Bremer K., Chase M.W., Reveal J.L., Soltis D.E., Soltis P.S., Stevens P.F., Anderberg A.A., Fay M.F., Goldblatt P., Judd W.S., Kallersjo M., Karehed J., Kron K.A., Lundberg J., Nickrent D.L., Olmstead R.G., Oxelman B., Pires J.C., Rodman J.E., Rudall P.J., Savolainen V., Sytsma K.J., van der Bank M., Wurdack K., Xiang J.Q.Y., and Zmarzty S. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141 (2003) 399-436
9. Cai Z., Penaflor C., Kuehl J.V., Leebens-Mack J., Carlson J., dePamphilis C.W., and Jansen R.K. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogeny of magnoliids. BMC Evol. Biol. 6 (2006) 77
10. Chang C.-C., Lin H.-C., Lin I.-P., Chow T.-Y., Chen H.-H., Chen W.-H., Cheng C.-H., Lin C.-Y., Liu S.-M., Chang C.-C., and Chaw S.-M. The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol. Biol. Evol. 23 (2006) 279-291
11. Chase M.W., Soltis D.E., Olmstead R., Morgan D., Les D., Mishler B., Duvall M., Price R., Hills H., Qui Y.-L., Kron K., Rettig J., Conti E., Palmer J., Manhart J., Sytsma K., Michaels H., Kress J., Karol K., Clark D., Hedren M., Gaut B., Jansen R.K., Kim K.-J., Wimpee C., Smith J., Furnier G., Straus S., Xiang Q.-Y., Plunkett G., Soltis P.S., Swensen S., Williams S., Gadek P., Quinn C., Equiarte L., Golenberg E., Learn Jr. G., Graham S., Barrett S., Dayanandan S., and Albert V. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann. Mo. Bot. Gard. 80 (1993) 528-580
12. Chase M.W., Fay M.F., Devey D., Maurin O., Rønsted N., Davies J., Pillon Y., Petersen G., Seberg O., Tamura M.N., Asmussen C.B., Hilu K., Borsch T., Davis J.I., Stevenson D.W., Pires J.C., Givnish T.J., Sytsma K.J., McPherson M.A., Graham S.W., and Rai H.S. Multigene analyses of monocot relationships: a summary. Aliso 22 (2005) 63-75
13. Chumley T.W., Palmer J.D., Mower J.P., Fourcade H.M., Calie P.J., Boore J.L., and Jansen R.K. The complete chloroplast genome sequence of Pelargonium × hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol. Biol. Evol. 23 (2006) 2175-2190
14. Cui L., Veeraraghavan N., Richer A., Wall K., Jansen R.K., Leebens-Mack J., Makalowska I., and dePamphillis C.W. ChloroplastDB: the chloroplast genome database. Nucleic Acids Res. 34 (2006) D692-D696
15. Daniell H., Lee S.-B., Grevich J., Saksi C., Quesada-Vargas T., Guda C., Tomkins J., and Jansen R.K. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor. Appl. Genet. 112 (2006) 1503-1518
16. Downie S.R., Olmstead R.G., Zurawski G., Soltis D.E., Soltis P.S., Watson J.C., and Palmer J.D. Six independent losses of the chloroplast DNA rpl2 intron in dicotyledons: molecular and phylogenetic implications. Evolution 45 (1991) 1245-1259
17. Doyle J.A., Eklund H., and Herendeen P.S. Floral evolution in Chloranthaceae: implications of a morphological phylogenetic analysis. Int. J. Plant Sci. 164 (2003) S365-S382
18. Doyle J.A., and Endress P.K. Morphological phylogenetic analysis of basal angiosperms: comparison and combination with molecular data. Int. J. Plant Sci. 161 (2000) S121-S153
19. Doyle J.J., Doyle J.L., and Palmer J.D. Multiple independent losses of two genes and one intron from legume chloroplast genomes. Syst. Bot. 20 (1995) 272-294
20. Eklund H., Doyle J.A., and Herendeen P.S. Morphological phylogenetic analysis of living and fossil Chloranthaceae. Int. J. Plant Sci. 165 (2004) 107-151
21. Edgar R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5 (2004) 1-19
22. Ewing B., and Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Gen. Res. 8 (1998) 186-194
23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
24. Goldman N., Anderson J.P., and Rodrigo A.G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49 (2000) 652-670
25. Gordon D., Abajian C., and Green P. Consed: a graphical tool for sequence finishing. Gen. Res. 8 (1998) 195-202
26. Goremykin V., Hirsch-Ernst K.I., Wolfl S., and Hellwig F.H. The chloroplast genome of the "basal" angiosperm Calycanthus fertilis - structural and phylogenetic analyses. Plant Syst. Evol. 242 (2003) 119-135
27. Goremykin V.V., Hirsch-Ernst K.I., Wolfl S., and Hellwig F.H. Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol. Biol. Evol. 20 (2003) 1499-1505
28. Goremykin V.V., Hirsch-Ernst K.I., Wolfl S., and Hellwig F.H. The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Mol. Biol. Evol. 21 (2004) 1445-1454
29. Goremykin V.V., Holland B., Hirsch-Ernst K.I., and Hellwig F.H. Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol. Biol. Evol. 22 (2005) 1813-1822
30. Goremykin V.V., and Hellwig F.H. A new test of phylogenetic model fitness addresses the issue of the basal angiosperm phylogeny. Gene 381 (2006) 81-91
31. Goulding S.E., Olmstead R.G., Morden C.W., and Wolfe K.H. Ebb and flow of the chloroplast inverted repeat. Mol. Gen. Genet. 252 (1996) 195-206
32. Graham S.W., and Olmstead R.G. Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. Am. J. Bot. 87 (2000) 1712-1730
33. Graham S.W., Reeves P.A., Burns A.C.E., and Olmstead R.G. Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. Int. J. Plant Sci. 161 (2000) S83-S96
34. Hamby R.K., and Zimmer E.A. Ribosomal RNA as a phylogenetic tool in plant systematics. In: Soltis P.S., Soltis D.E., and Doyle J.J. (Eds). Molecular Systematics of Plants (1992), Chapman and Hall, New York 50-91
35. Hilu K.W., Borsch T., Muller K., Soltis D.E., Soltis P.S., Savolainen V., Chase M., Powell M., Alice L., Evans R., Sauquet H., Neinhuis C., Slotta T., Rohwer J., and Chatrou L. Inference of angiosperm phylogeny based on matK sequence information. Am. J. Bot. 90 (2003) 1758-1776
36. Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., Mori M., Kondo C., Honji Y., Sun C.R., Meng B.Y., Li Y.Q., Kanno A., Nishizawa Y., Hirai A., Shinozaki K., and Sugiura M. 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 (1989) 185-194
37. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
38. Hupfer H., Swaitek M., Hornung S., Herrmann R.G., Maier R.M., Chiu W.L., and Sears B. Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome 1 of the five distinguishable Euoenthera plastomes. Mol. Gen. Genet. 263 (2000) 581-585
39. Jansen R.K., Kaittanis C., Saski C., Lee S.B., Tomkins J., Alverson A.J., and Daniell H. 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 (2006) 32
40. Jansen R.K., Raubeson L.A., Boore J.L., dePamphilis C.W., Chumley T.W., Haberle R.C., Wyman S.K., Alverson A.J., Peery R., Herman S.J., Fourcade H.M., Kuehl J.V., McNeal J.R., Leebens-Mack J., and Cui L. Methods for obtaining and analyzing chloroplast genome sequences. Methods Enzymol. 395 (2005) 348-384
41. Kato T., Kaneko T., Sato S., Nakamura Y., and Tabata S. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 7 (2000) 323-330
42. Kim K.-J., and Lee H.-L. Complete chloroplast genome sequence from Korean Ginseng (Panax schiseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 11 (2004) 247-261
43. Kim Y.D., and Jansen R.K. Characterization and phylogenetic distribution of chloroplast DNA rearrangement in the Berberidaceae. Plant Syst. Evol. 190 (1994) 157-185
44. Kurtz S., Choudhuri J.V., Ohlebusch E., Schleiermacher C., Stoye J., and Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29 (2001) 4633-4642
45. Lavin M., Doyle J.J., and Palmer J.D. Systematic and evolutionary significance of the loss of the large chloroplast DNA inverted repeat in the family Leguminosae. Evolution 44 (1990) 390-402
46. Lee H.-L., Jansen R.K., Chumley T.W., and Kim K.-J. Apparent gene translocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol. Biol. Evol. 24 (2007) 1161-1180
47. Lee S.B., Kaittanis C., Jansen R.K., Hostetler J.B., Tallon L.J., Town C.D., and Daniell H. The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics 7 (2006) 61
48. Leebens-Mack J., Raubeson L.A., Cui L.Y., Kuehl J.V., Fourcade M.H., Chumley T.W., Boore J.L., Jansen R.K., and dePamphilis C.W. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Mol. Biol. Evol. 22 (2005) 1948-1963
49. Lockhart P.J., and Penny D. The place of Amborella within the radiation of angiosperms. Trends Plant Sci. 10 (2005) 201-202
50. Maddison, D.R., Maddison, W.P., 2005. MacClade. Version 4.08. Sinauer Associates, Sunderland, Massachusetts.
51. Maier R.M., Neckermann K., Igloi G.L., and Kossel H. 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 (1995) 614-628
52. Mathews S., and Donoghue M.J. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286 (1999) 947-950
53. Mathews S., and Donoghue M.J. Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. Int. J. Plant Sci. 161 (2000) S41-S55
54. McNeal J.R., Leebens-Mack J.H., and dePamphilis C.W. Utilization of fosmid partial genomic libraries for sequencing complete organellar genomes. Biotechniques 41 (2006) 69-73
55. Moore M.J., Dhingra A., Soltis P., Shaw R., Farmerie W.G., Folta K.M., and Soltis D.E. Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol. 6 (2006) 17
56. Nagano Y., Matsuno R., and Sasaki Y. Sequence and transcriptional analysis of the gene cluster trnQ-zfpA-psaI-ORF231-petA in pea chloroplasts. Curr. Genet. 20 (1991) 431-436
57. Ogihara Y., Isono K., Kojima T., Endo A., Hanaoka M., Shiina T., Terachi T., Utsugi S., Murata M., Mori N., Takumi S., Ikeo K., Gojobori T., Murai R., Murai K., Matsuoka Y., Ohnishi Y., Tajiri H., and Tsuenewaki K. Chinese spring wheat (Triticum aestivum L.) chloroplast genome: complete sequence and contig clones. Plant Mol. Biol. Rep. 18 (2000) 243-253
58. Ohyama K., Fukuzawa H., Kohchi T., Shirai H., Sano T., Sano S., Umesono K., Shiki Y., Takeuchi M., Chang Z., Aota S., Inokuchi H., and Ozeki H. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322 (1986) 572-574
59. Palmer J.D. Isolation and structural analysis of chloroplast DNA. Methods Enzymol. 118 (1986) 167-186
60. Palmer J.D. Plastid chromosomes: structure and evolution. In: Bogorad L., and Vasil I. (Eds). Cell Culture and Somatic Cell Genetics of Plants (1991), Academic Press, San Diego, California, USA 5-53
61. Palmer J.D., and Thompson W.F. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell 29 (1982) 537-550
62. Palmer J.D., Nugent J.M., and Herbon L.A. 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 (1987) 769-773
63. Palmer J.D., Osorio B., Aldrich J., and Thompson W.F. Chloroplast DNA evolution among legumes - loss of a large inverted repeat occurred prior to other sequence rearrangements. Curr. Genet. 11 (1987) 275-286
64. Palmer J.D., and Stein D.B. Conservation of chloroplast genome structure among vascular plants. Curr. Genet. 10 (1986) 823-833
65. Plunkett G.M., and Downie S.R. Expansion and contraction of the chloroplast inverted repeat in Apiaceae subfamily Apioideae. Syst. Bot. 25 (2000) 648-667
66. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
67. Price R.A., Calie P.J., Downie S.R., Logsdon J.M., and Palmer J.D. Chloroplast DNA variation in the Geraniaceae - a preliminary report. In: Vorster P. (Ed). The International Geraniaceae Symposium (1990), The University of Stellenbosch, Republic of South Africa
68. Qiu Y.-L., Chase M.W., Les D.H., and Parks C.R. Molecular phylogenetics of the Magnoliidae: cladistic analyses of nucleotide sequences of the plastid gene rbcL. Ann. Mo. Bot. Gard. 80 (1993) 587-606
69. Qiu Y.-L., Lee J., Bernasconi-Quadroni F., Soltis D.E., Soltis P.S., Zanis M., Zimmer E.A., Chen Z., Savolainen V., and Chase M.W. Phylogeny of basal angiosperms: analyses of five genes from three genomes. Int. J. Plant Sci. 161 (2000) S3-S27
70. Qiu Y.L., Lee J., Bernasconi-Quadroni F., Soltis D.E., Soltis P.S., Zanis M., Zimmer E.A., Chen Z.D., Savolainen V., and Chase M.W. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402 (1999) 404-407
71. Qiu Y.-L., Lee J., Whitlock B.A., Bernasconi-Quadroni F., and Dombrovska O. Was the ANITA rooting of the angiosperm phylogeny affected by long branch attraction?. Mol. Biol. Evol. 18 (2001) 1745-1753
72. Qiu Y.L., Dombrovska O., Lee J., Li L.B., Whitlock B.A., Bernasconi-Quadroni F., Rest J.S., Davis C.C., Borsch T., Hilu K.W., Renner S.S., Soltis D.E., Soltis P.S., Zanis M.J., Cannone J.J., Gutell R.R., Powell M., Savolainen V., Chatrou L.W., and Chase M.W. Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. Int. J. Plant Sci. 166 (2005) 815-842
73. Qiu Y.-L., Li L., Hendry T., Li R., Taylor D.W., Issa M.J., Ronen A.J., Vekaria M.L., and White A.M. Reconstructing the basal angiosperm phylogeny: evaluating information content of the mitochondrial genes. Taxon 55 (2006) 837-856
74. Raubeson L.A., and Jansen R.K. Chloroplast genomes of plants. In: Henry R. (Ed). Diversity and Evolution of Plants - Genotypic and Phenotypic Variation in Higher Plants (2005), CABI Publishing, UK 45-68
75. Raubeson L.A., Peery R., Chumley T.W., Dziubek C., Fourcade H.M., Boore J.L., and Jansen R.K. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8 (2007) 174
76. Ruhlman T., Lee S.-B., Jansen R.K., Hostetler J.B., Tallon L.J., Town C.D., and Daniell H. Complete chloroplast genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7 (2006) 222
77. Saski C., Lee S.-B., Daniell H., Wood T.C., Tomkins J., Kim H.-G., and Jansen R.K. Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol. Biol. 59 (2005) 309-322
78. Saski C., Lee S.-B., Fjellheim S., Guda C., Jansen R.K., Luo H., Tomkins J., Rognli O.A., Daniell H., and Clarke J.L. Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera and comparative analyses with other grass genomes. Theor. Appl. Genet. (2007) 10.1007/s00122-007-0567-4
79. Sato S., Nakamura Y., Kaneko T., Asamizu E., and Tabata S. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6 (1999) 283-290
80. Savolainen V., Chase M.W., Morton C.M., Soltis D.E., Bayer C., Fay M.F., De Bruijn A., Sullivan S., and Qiu Y.-L. Phylogenetics of flowering plants based upon a combined analysis of plastid atpB and rbcL gene sequences. Syst. Biol. 49 (2000) 306-362
81. Schmitz-Linneweber C., Maier R.M., Alcaraz J.P., Cottet A., Herrmann R.G., and Mache R. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45 (2001) 307-315
82. Schmitz-Linneweber C., Regel R., Du T.G., Hupfer H., Herrmann R.G., and Maier R.M. The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol. Biol. Evol. 19 (2002) 1602-1612
83. Shen G.F., Chen K., Wu M., and Kung S.D. Nicotiana chloroplast genome IV. N. accuminata has larger inverted repeats and genome size. Mol. Gen. Genet. 187 (1982) 12-18
84. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
85. Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K., Ohto C., Torazawa K., Meng B.Y., Sugita M., Deno H., Kamogashira T., Yamada K., Kusuda J., Takaiwa F., Kato A., Tohdoh N., Shimada H., and Sugiura M. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5 (1986) 2043-2049
86. Soltis D.E., and Soltis P.S. Amborella not a "basal angiosperm"? Not so fast. Am. J. Bot. 91 (2004) 997-1001
87. Soltis P.S., and Soltis D.E. The origin and diversification of angiosperms. Am. J. Bot. 91 (2004) 1614-1626
88. Soltis P.S., Soltis D.E., and Chase M.W. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402 (1999) 402-404
89. Soltis D.E., Soltis P.S., Chase M.W., Mort M.W., Albach D.C., Zanis M., Savolainen V., Hahn W.H., Hoot S.B., Fay M.F., Axtell M., Swensen S.M., Prince L.M., Kress W.J., Nixon K.J., and Farris J.S. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 133 (2000) 381-461
90. Soltis D.E., Albert V.A., Savolainen V., Hilu K., Qiu Y.L., Chase M.W., Farris J.S., Stefanovic S., Rice D.W., Palmer J.D., and Soltis P.S. Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics. Trends Plant Sci. 9 (2004) 477-483
91. Soltis P.S., Endress P.K., Chase M.W., and Soltis D.E. Phylogeny and Evolution of Angiosperms (2005), Sinauer Associates, Inc., Sunderland, MA, USA
92. Soltis D.E., Gitzendanner M.A., and Soltis P.S. A 567-taxon data set for angiosperms: the challenge posed by Bayesian analyses of large data sets. Int. J. Plant Sci. 168 (2007) 137-157
93. Steane D.A. Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae). DNA Res. 12 (2005) 215-220
94. Stefanovic S., and Olmstead R.G. Down the slippery slope: plastid genome evolution in Convolvulaceae. J. Mol. Evol. 61 (2005) 292-305
95. Stefanovic S., Rice D.W., and Palmer J.D. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?. BMC Evol. Biol. 4 (2004) 35
96. Sugiura M. The Chloroplast Genome. Plant Mol. Biol. 19 (1992) 149-168
97. *. Phylogenetic analysis using parsimony (* and other methods). Version 4.10. Sinauer Associates, Sunderland, Massachusetts.
98. Tsudzuki J., Nakashima K., Tsudzuki T., Hiratsuka J., Shibata M., Wakasugi T., and Sugiura M. Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16. Mol. Gen. Genet. 232 (1992) 206-214
99. Tuskan G.A., Difazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., Schein J., Sterck L., Aerts A., Bhalerao R.R., Bhalerao R.P., Blaudez D., Boerjan W., Brun A., Brunner A., Busov V., Campbell M., Carlson J., Chalot M., Chapman J., Chen G.L., Cooper D., Coutinho P.M., Couturier J., Covert S., Cronk Q., Cunningham R., Davis J., Degroeve S., Dejardin A., de Pamphilis C., Detter J., Dirks B., Dubchak I., Duplessis S., Ehlting J., Ellis B., Gendler K., Goodstein D., Gribskov M., Grimwood J., Groover A., Gunter L., Hamberger B., Heinze B., Helariutta Y., Henrissat B., Holligan D., Holt R., Huang W., Islam-Faridi N., Jones S., Jones-Rhoades M., Jorgensen R., Joshi C., Kangasjarvi J., Karlsson J., Kelleher C., Kirkpatrick R., Kirst M., Kohler A., Kalluri U., Larimer F., Leebens-Mack J., Leple J.C., Locascio P., Lou Y., Lucas S., Martin F., Montanini B., Napoli C., Nelson D.R., Nelson C., Nieminen K., Nilsson O., Pereda V., Peter G., Philippe R., Pilate G., Poliakov A., Razumovskaya J., Richardson P., Rinaldi C., Ritland K., Rouze P., Ryaboy D., Schmutz J., Schrader J., Segerman B., Shin H., Siddiqui A., Sterky F., Terry A., Tsai C.J., Uberbacher E., Unneberg P., Vahala J., Wall K., Wessler S., Yang G., Yin T., Douglas C., Marra M., Sandberg G., Van de Peer Y., and Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313 (2006) 1596-1604
100. Wakasugi T., Tsudzuki J., Ito S., Nakashima K., Tsudzuki T., and Sugiura M. 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 (1994) 9794-9798
101. Wilgenbusch, J.C., Warren, D.L., Swofford, D.L., 2004. AWTY: a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. .
102. Wolfe K.H. The site of deletion of the inverted repeat in pea chloroplast DNA contains duplicated gene fragments. Curr. Genet. 13 (1988) 97-99
103. Wu C.-S., Wang Y.-N., Liu S.-M., and Chaw S.-M. Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parviflorum: insights into cpDNA evolution and phylogeny of extant seed plants. Mol. Biol. Evol. 24 (2007) 1366-1379
104. Wyman S.K., Jansen R.K., and Boore J.L. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20 (2004) 3252-3255
105. Zanis M.J., Soltis D.E., Soltis P.S., Mathews S., and Donoghue M.J. The root of the angiosperms revisited. Proc. Natl. Acad. Sci. USA 99 (2002) 6848-6853
106. Zanis M.J., Soltis P.S., Qiu Y.-L., Zimmer E.A., and Soltis D.E. Phylogenetic analyses and perianth evolution in basal angiosperms. Ann. Mo. Bot. Gard. 90 (2003) 129-150
107. Zhang L.B., and Renner S. The deepest splits in Chloranthaceae as resolved by chloroplast sequences. Int. J. Plant Sci. 164 (2003) S383-S392
108. Zwickl, D.J., 2006. GARLI (Genetic Algorithm for Rapid Likelihood Inference). Version 0.942 (www.bio.utexas.edu/faculty/antisense/garli/Garli.html).