Potential Phylogenetic Utility of the Low-Copy Nuclear Gene pistillata in Dicotyledonous Plants: Comparison to nrDNA ITS and trnL Intron in Sphaerocardamum and Other Brassicaceae

Molecular Phylogenetics and Evolution

Volumn 13, Issue 1, 1999, Pages 20-30

  Bailey, C Donovan ^a   Doyle, Jeff J ^a  

^a Department of Population Medicine and Diagnostic Sciences   (United States)

Author keywords

Brassicaceae; MADS box; nrDNA ITS; pistillata; phylogeny; Sphaerocardamum; trnL intron.

Indexed keywords

ARABIDOPSIS PROTEIN; HOMEODOMAIN PROTEIN; MADS DOMAIN PROTEIN; PISTILLATA PROTEIN, ARABIDOPSIS; PLANT DNA; PRIMER DNA; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ARTICLE; BRASSICACEAE; CELL NUCLEUS; CHLOROPLAST; CLASSIFICATION; COMPARATIVE STUDY; GENE; GENETIC VARIABILITY; GENETICS; INTRON; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ARABIDOPSIS PROTEINS; BASE SEQUENCE; BRASSICACEAE; CELL NUCLEUS; CHLOROPLASTS; DNA PRIMERS; DNA, PLANT; GENES, PLANT; HOMEODOMAIN PROTEINS; INTRONS; MADS DOMAIN PROTEINS; PHYLOGENY; PLANT PROTEINS; TRANSCRIPTION FACTORS; VARIATION (GENETICS);

EID: 0033209648     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1999.0627     Document Type: Article

References (56)

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment tool. J. Mol. Biol. 215:1990;403-410.
2. Atkinson R. G., Cipriani G., Whittaker D. J., Gardner R. C. The allopolyploid origin of kiwifruit, Actinidia deliciosa (Actinidiaceae). Plant Syst. Evol. 205:1997;111-124.
3. Baldwin B. G., Sanderson M. J., Porter M. J., Wojciechowski M. F., Campbell C. S., Donoghue M. J. The ITS region of the nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann. Mo. Bot. Gard. 82:1995;247-277.
4. Buckler E. S. IV, Ippolito A., Holtsford T. P. The evolution of ribosomal DNA: Divergent paralogues and phylogenetic implications. Genetics. 145:1997;821-832.
5. Campbell C. S., Wojciechowski M. F., Baldwin B. G., Alice L. A., Donoghue M. J. Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Mol. Biol. Evol. 14:1997;81-90.
6. Clegg M. T., Cummings M. P., Durbin M. L. The evolution of plant nuclear genes. Proc. Natl. Acad. Sci. USA. 94:1997;7791-7798.
7. Coen E. S., Momero J. M., Doyle S., Elliot R., Murphy G., Carpenter R. floricaula: A homeotic gene required for flower development in Antirrhinum majus. Cell. 63:1990;1311-1322.
8. Denton A. L., Hall B. D., McConaughy B. L. rpb2, a nuclear gene for tracing angiosperm phylogeny. Am. J. Bot. 83S:1996;150.
9. Doyle J. J., Doyle J. L. Isolation of plant DNA from fresh tissue. Focus. 12:1990;13-15.
10. Doyle J. J., Kanazin V., Shoemaker R. C. Phylogenetic utility of histone H3 intron sequences in the perennial relatives of soybean (Glycine: Leguminosae). Mol. Phylogenet. Evol. 6:1996;438-447.
11. Doyle J. J., Doyle J. L. The cytosolic glutamine synthetase gene family in Leguminosae: Gene phylogeny and evolution of its role in nodulation. Am. J. Bot. 84S:1997;188.
12. Doyle J. J. Evolution of a plant homeotic multigene family: Toward connecting molecular systematics and molecular developmental genetics. Syst. Biol. 43:1994;307-328.
13. Fangan B. M., Stedje B., Stabbetorp O. E., Jensen E. S., Jakobsen K. S. A general approach for PCR-amplification and sequencing of chloroplast DNA from crude vascular plant algal tissue. BioTechniques. 16:1994;484-494.
14. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 39:1985;783-791.
15. Galloway G. L., Malmberg R. L., Price R. A. Phylogenetic utility of the nuclear gene argenine decarboxylase, with an example from the Brassicaceae. Am. J. Bot. 84S:1997;196.
16. Gielly L., Yuan Y. M., Kupfer P., Taberlet P. Phylogenetic use of noncoding regions in the genus Gentiana L.: Chloroplast trnL (UAA) intron versus nuclear ribosomal internal transcribed spacer sequences. Mol. Phylogenet. Evol. 5:1996;460-466.
17. Goloboff, P. 1993 Copyright; Upgraded 1996, Nona Computer Software version 1.5.1. Published by, Author, NY.
18. Goto K., Meyerowitz E. M. Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes Dev. 8:1994;1548-1560.
19. Kim K. J., Jansen R. K. Comparison of phylogenetic hypotheses among different datasets in dwarf dandelions (Krigia, Asteraceae): Additional information from the internal transcribed spacer sequences of nuclear ribosomal DNA. Plant Syst. Evol. 190:1994;157-185.
20. Kramer E. M., Dorit R. L., Irish V. F. Molecular evolution of genes controlling petal and stamen development: Duplication and divergence within APETALA3 and PISTILLATA MADS-box gene lineages. Genetics. 149:1998;765-783.
21. Lagercrantz U. J., Putterill J., Coupland G., Lydiate D. Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time. Plant J. 9:1996;13-20.
22. Li W. H. Molecular Evolution. 1997;Sinauer, Sunderland.
23. Ma H., Yanofsky M. F., Meyerowitz M. E. AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes. Genes Dev. 5:1991;484-495.
24. Mandel M. A., Gustafson-Brown C., Savidge B., Yanofsky M. F. Molecular characterization of the Arabidopsis floral homeotic gene APETALA1. Nature. 360:1992;273-277.
25. Mason-Gamer R. J., Kellogg E. A. Potential utility of the nuclear gene waxy for plant phylogenetic analyses. Am. J. Bot. 83S:1996;178.
26. Mathews S., Lavin M., Sharrock R. A. Evolution of the phytochrome gene family and its utility for phylogenetic analyses of angiosperms. Ann. Mo. Bot. Gard. 82:1995;296-321.
27. Meyerowitz E. M. Structure and organization of the Arabidopsis thaliana nuclear genome. Meyerowitz E., Sommerville C. Arabidopsis. 1994;21-36 Cold Springs Harbor Laboratory Press, Cold Springs Harbor.
28. Morton B. R., Gaut B., Clegg M. T. Evolution of alcohol dehydrogenase gene in the Palm and Grass Families. Proc. Natl. Acad. Sci. USA. 93:1996;11735-11739.
29. Münster T., Pahnke J., Di Rosa A., Kim J. T., Martin W., Saedler H., Theissen G. Floral homeotic genes were recruited from homologous MADS-box genes preexisting in the common ancestor of ferns and seed plants. Proc. Natl. Acad. Sci. USA. 94:1997;2415-2420.
30. Neuffer B., Eschner S. Life-history and ploidy levels in the genus Capsella (Brassicaceae). Can. J. Bot. 73:1995;1354-1365.
31. Nixon, K. C. 1993a, DADA matrix editing program. Published by, author, Trumansburg, New York.
32. Nixon, K. C. 1993b, Clados computer software version 1.4. Published by, author, Trumansburg, New York.
33. O'Kane S. L. Jr., Schaal B. A., Al-Shehbaz I. A. The origins of Arabidopsis suecica (Brassicaceae), as indicated by nuclear rDNA sequences. Syst. Bot. 21:1996;559-566.
34. Olmstead R. G., Palmer J. D. Chloroplast DNA systematics: A review of methods and data analysis. Am. J. Bot. 81:1994;1205-1224.
35. Peralta I. E., Ballard H., Spooner D. M. "Waxy" gene intron phylogeny of tomatoes, Solanum subsect. Lycopersicum (Solanaceae). Am. J. Bot. 84S:1997;222.
36. Purugganan M. D., Roundley S. D., Schmidt R. J., Yanofsky M. F. Molecular evolution of flower development: Diversification of the plant MADS-box regulatory gene family. Genetics. 140:1995;345-356.
37. Rollins R. C. Sphaerocardamum (Cruciferae). Contrib. Gray Herbarium. 213:1984;11-17.
38. Rollins R. C. The Continental Cruciferae of North America. 1993;Stanford Univ. Press, Stanford.
39. Sang T., Donoghue M. J., Zhang D. Evolution of alcohol dehydrogenase genes in Peonies (Paeonia): Phylogenetic relationships of putative nonhybrid species. Mol. Biol. Evol. 14:1997;994-1007.
40. Sanderson M. J., Doyle J. J. Reconstruction of organismal and gene phylogenies from data on multigene families: Concerted evolution, homoplasy, and confidence. Syst. Biol. 41:1992;4-17.
41. Schilling E. E., Panero J. L. Phylogenetic reticulation in subtribe Helianthinae. Am. J. Bot. 83:1996;939-948.
42. Sieburth L. E., Meyerowitz E. M. Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. Plant Cell. 9:1997;355-365.
43. Small R., Ryburn J., Cronn R., Seelanan T., Wendel J. F. Molecular phylogenetics of recently diverged groups: Evidence from nuclear and plastid sequences. Am. J. Bot. 84S:1997;231-232.
44. Soltis D. E., Kuzoff R. K. Discordance between nuclear and chloroplast phylogenies in the Heuchera group (Saxifragaceae). Evolution. 49:1995;727-742.
45. Soltis D. E., Soltis P. S. Choosing an approach and an appropriate gene for phylogenetic analysis. Soltis D. E., Soltis P. S., Doyle J. J. Molecular Systematics of Plants, II, DNA Sequencing. 1998;1-42 Kluwer Academic, Dordrecht.
46. Swofford, D. L. (unpubl.), PAUP*: Phylogenetic Analysis Using Parsimony. Computer program distributed by the the, Illinois Natural History Survey, Champaign, IL.
47. Taberlet P., Gielly L., Pautou G., Bouvet J. Universal primers for amplification of three noncoding regions of chloroplast DNA. Plant Mol. Biol. 17:1991;1105-1109.
48. Tandre K., Albert V. A., Sundas A., Engstrom P. Conifer homologues to genes that control floral development in angiosperms. Plant Mol. Biol. 27:1995;69-78.
49. Teutonico R. A., Osborn T. C. Mapping of RFLP and qualitative trait loci in Brassica rapa and comparison to the linkage maps of B. napus, B. oleracea, and Arabidopsis thaliana. Theor. Appl. Genet. 89:1994;885-894.
50. Theissen G., Kim J. T., Saedler H. Classification and phylogeny of the MADS-Box multigene family suggest defined roles of MADS-Box gene subfamilies in the morphological evolution of Eukaryotes. J. Mol. Evol. 43:1996;484-516.
51. Troebner W., Ramirez L., Motte P. H. I., Huijser P., Loennig W. E., Saedler H., Sommer H., Schwarz-Sommer Z. GLOBOSA: A homeotic gene which interacts with DEFICIENS in the control of Antirrhinum floral organogenesis. EMBO J. 11:1992;4693-4707.
52. Wendel J. F., Schnabel A., Seelanan T. An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Mol. Phylogenet. Evol. 4:1995;298-313.
53. Wheeler, W, and, Gladstein, D. 1993, MALIGN DNA sequence alignment software version 1.99. Published by, authors, New York.
54. White T. J., Bruns T., Lee S., Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Innis M., Gelfand D., Sninsky J., White T. PCR Protocols: A Guide to Methods and Applications. 1990;315-322 Academic Press, San Diego.
55. Yanofsky M. F., Ma H., Bowman J. L., Drews G. N., Feldmann K. A., Meyerowitz E. M. The protein encoded by Arabidopsis homeotic gene agamous resembles transcription factors. Nature. 346:1990;35-39.
56. Zhang D. X., Hewitt G. M. Insect mitochondrial control region: A review of its structure, evolution, and usefulness in evolutionary studies. Biochem. Syst. Ecol. 25:1997;99-120.