Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm

Molecular Biology and Evolution

Volumn 20, Issue 9, 2003, Pages 1499-1505

  Goremykin, Vadim V ^a   Hirsch Ernst, Karen I ^b   Wölfl, Stefan ^a   Hellwig, Frank H ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

Amborella; Angiosperms; Chloroplast genomes; Gymnosperms; Molecular evolution; Substitution rates

Indexed keywords

CHLOROPLAST DNA; PROTEIN;

ANGIOSPERM; ARTICLE; BOTANY; CHLOROPLAST GENETICS; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS;

ANGIOSPERMS; CHLOROPLASTS; EVOLUTION; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; PHYLOGENY; TREES;

AMBORELLA; AMBORELLA TRICHOPODA; DICOTYLEDONEAE; GYMNOSPERMAE; MAGNOLIOPHYTA; PINUS THUNBERGII; TRICHOPODA;

EID: 0041834716     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg159     Document Type: Article

References (51)

1. Arber, E. A. N., and J. Parkin. 1907. On the origin of angiosperms. J. Linnean Soc. 38:29-80.
2. -. 1908. Studies on the evolution of angiosperms: the relationship of the angiosperms to Gnetales. Ann. Bot. (London) 22:489-515.
3. Bailey, I. W., and B. G. L. Swamy. 1948. Amborella trichopoda Baill: a new morphological type of vesselless dicotyledons. J. Arnold Arb. 29:245-254.
4. Baillon, H. 1869. Histoire des plantes. Vol. I. L. Hachette & Cie. Paris, London, Leipzig.
5. Barkman, T. J., G. Chenery, J. R. McNeal, J. Lyons-Weiler, W. J. Ellisens, G. Moore, A. D. Wolfe, and C. W. dePamphilis, 2000. Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. Proc. Natl. Acad. Sci. USA 97:13166-13171.
6. Bentham, G., and J. D. Hooker. 1880. Genera plantarum, III(1). Reeve & Company, London.
7. Cronquist, A. 1981. An integrated system of classification of flowering plants. Columbia University Press, New York.
8. Dayhoff, M. O., R. M. Schwartz, and B. C. Orcutt. 1978. A model of evolutionary change in proteins. Pp. 345-352 in M. O. Dayhoff, ed. Atlas of protein sequence structure, Vol. 5, Suppl. 3. National Biomedical Research Foundation, Washington, D.C.
9. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using PHRED. I. Accuracy assessment. Genome Res. 8:175-185.
10. Felsenstein, J. 1989. PHYLIP - phylogeny inference package. Version 3.2. Cladistics 5:164-166.
11. Floyd, S. K., and W. E. Friedman. 2001. Developmental evolution of endosperm in basal angiosperms: evidence from Amborella (Amborellaceae), Nuphar (Nymphaeaceae), and Illicium (Illiciaceae). Plant Syst. Evol. 228:153-169.
12. Goremykin, V., K. I. Hirsch-Ernst, S. Wölfl, and F. H. Hellwig. 2003. The chloroplast genome of the "basal" angiosperm Calycanthus fertilis - structural and phylogenetic analyses. Plant Syst. Evol. (in press).
13. Graham, S. W., and R. G. Olmstead. 2000. Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. Am. J. Bot. 87:1712-1730.
14. Henikoff, S., and J. G. Henikoff. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89:10915-10919.
15. Hiratsuka, J., H. Shimada, R. Whittier et al. (16 co-authors). 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.
16. Hupfer, H., M. Swiatek, S. Hornung, R. G. Hermann, R. M. Maier, W-L. Chiu, and B. Sears. 2000. Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable Euoenothera plastomes. Mol. Gen. Genet. 263:581-585.
17. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
18. Kato, T., T. Kaneko, S. Sato, Y. Nakamura, and S. Tabata. 2000. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 7:323-330.
19. Lockhart, P. J., C. J. Howe, A. C. Barbrook, A. W. D. Larkum, and D. Penny. 1999. Spectral analysis, systematic bias, and the evolution of chloroplasts. Mol. Biol. Evol. 16:573-576.
20. Maier, R. M., K. Neckermann, G. L. Igloi, and H. Kossel. 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.
21. Martin, W., B. Stoebe, V. Goremykin, S. Hansmann, M. Hasegawa, and K. V. Kowallik. 1998. Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393:162-165.
22. Meyen, S. V. 1986. Hypothesis of the origin of the angiosperms from Bennetitales by gamoheterotrophy: transition of characters from one sex to another. Zh. Obshzh. Biol. 47:291-309 [in Russian].
23. Money, L. L., I. W. Bailey, and B. G. L. Swamy. 1952. The morphology and relationships of the Monimiaceae. J. Arnold Arb. 31:372-404.
24. Müller, T., and M. Vingron. 2000. Modeling amino acid replacement. J. Comput. Biol. 7:761-776.
25. Murray, M. G., and W. F. Thompson. 1980 Rapid isolation of high molecular weight DNA. Nucleic Acids Res. 8:4321-4325.
26. Ogihara, Y., K. Isono, T. Kojim et al. (19 co-authors). 2002. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol. Genet. Genomics. 266:740-746.
27. Ohtani, K., H. Yamamoto, and K. Akimitsu. 2002. Sentitivity to Alternaria alternata toxin in citrus because of altered mitochondrial RNA processing. Proc. Natl. Acad. Sci. USA 99:2439-2444.
28. Ohyama, K., H. Fukuzawa, T. Kohchi et al. (13 co-authors). 1986. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572-574.
29. Parkinson, C. L., K. L. Adams, and J. D. Palmer. 1999. Multigene analyses identify the three earliest lineages of extant flowering plants. Curr. Biol. 9:1485-1488.
30. Pax, F. 1889. Monimiaceae. Pp. 94-105 in A. Engler and K. Prantl, eds. Die Natürlichen Pflanzenfamilien, III(2). W. Engelmann, Leipzig.
31. Perkins, J., and E. Gilg. 1901. Monimiaceae. Pp 1-122 in A. Engler, ed. Das Pflanzenreich, V(101). W. Engelmann, Leipzig.
32. Perkins, J. 1925. Übersicht über die Gattungen der Monimiaceae. W. Engelmann, Leipzig.
33. Pichon, P. 1948. Les Monimiacées, famille hété rogène. Bull. Mus. Nat. Hist. Nat. Paris 20:383-384.
34. Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
35. -. 2001. Simple (wrong) models for complex trees: a case from retroviridae. Mol. Biol. Evol. 18:271-275.
36. Qiu, Y-L., J. Lee, F. Bernasconi-Quadroni, D. E. Soltis, P. S. Soltis, M. Zanis, E. A. Zimmer, Z. Chen, V. Savolainen, and M. W. Chase. 1999. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402:404-407.
37. Sato, S., Y. Nakamura, T. Kaneko, E. Asamizu, and S. Tabata. 1999. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6:283-290.
38. Schmitz-Linneweber, C., R. M. Maier, J. P. Alcaraz, A. Cottet, R. G. Herrmann, and R. Mache. 2001. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45:307-315.
39. Shinozaki, K., M. Ohme, M. Tanaka et al. (23 co-authors). 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5:2043-2049
40. Soltis, P. S., D. E. Soltis, and M. W. Chase. 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402:402-403.
41. Staden, R., K. F. Beal, and J. K. Bonfield. 2000. The Staden package, 1998. Methods Mol. Biol. 132:115-130.
42. Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
43. Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
44. Takhtajan, A. 1966. Systema et phylogenia Magnoliophytorum. Nauka, Moscow, Leningrad.
45. Van de Peer, Y., and R. De Wachter. 1994. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10:569-570.
46. von Wettstein, R. 1924. Handbuch der systematischen Botanik. 3rd edition. Franz Deutige, Leipzig.
47. Wakasugi, T., J. Tsudzuki, S. Ito, K. Nakashima, T. Tsudzuki, and M. Sugiura. 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.
48. Whelan, S., and N. Goldman. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18:691-699.
49. Williams, J. H., and W. E. Friedman. 2002. Identification of diploid endosperm in an early angiosperm lineage. Nature. 415:522-526.
50. Yang, Z. 1997a. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
51. -. 1997b. How often do wrong models produce better phylogenies? Mol. Biol. Evol. 14:105-108.