Molecular evolution of FLORICAULA/LEAFY orthologs in the Andropogoneae (Poaceae)

Molecular Biology and Evolution

Volumn 22, Issue 4, 2005, Pages 1082-1094

  Bomblies, Kirsten ^a,b   Doebley, John F ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

Andropogoneae; Domestication; FLORICAULA LEAFY; Maize; zfl1; zfl2

Indexed keywords

ANDROPOGON; ARTICLE; DOMESTICATION; GENE CONTROL; GENE LOCUS; GENE SEQUENCE; GENETIC SELECTION; GENETIC VARIABILITY; GRASS; INFLORESCENCE; INTRON; MAIZE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT MORPHOLOGY; POACEAE; SORGHUM; TETRAPLOIDY;

BASE SEQUENCE; DNA PRIMERS; EVOLUTION, MOLECULAR; GENES, PLANT; PHYLOGENY; POACEAE;

EID: 16344364319     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi095     Document Type: Article

References (77)

1. Ahearn, K. P., H. A. Johnson, D. Weigel, and D. R. Wagner. 2001. NFL1, a Nicotiana tabacum LEAFY-like gene, controls meristem initiation and floral structure. Plant Cell Physiol. 42: 1130-1139.
2. Baumlein, H., I. Nagy, R. Villarroel, D. Inze, and U. Wobus. 1992. Cis-analysis of a seed protein gene promoter: the conservative RY repeat CATGCATG within the legumin box is essential for tissue-specific expression of a legumin gene. Plant J. 2: 233-239.
3. Bomblies, K., R. L. Wang, B. A. Ambrose, R. J. Schmidt, R. B. Meeley, and J. Doebley. 2003. Duplicate FLORICAULA/LEAFY homologs zfl1 and zfl2 control inflorescence architecture and flower patterning in maize. Development 130: 2385-2395.
4. Bray, N., I. Dubchak, and L. Pachter. 2003. AVID: a global alignment program. Genome Res. 13:97-102.
5. Bremer, K. 2000. Early Cretaceous lineages of monocot flowering plants. Proc. Natl. Acad. Sci. USA 97:4707-4711.
6. Clark, R. M., E. Linton, J. Messing, and J. F. Doebley. 2004. Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc. Natl. Acad. Sci. USA 101: 700-707.
7. Coen, E. S., J. M. Romero, S. Doyle, R. Elliott, G. Murphy, and R. Carpenter. 1990. floricaula: a homeotic gene required for flower development in Antirrhinum majus. Cell 63:1311-1322.
8. Conant, G. C., and A. Wagner. 2003. Asymmetric sequence divergence of duplicate genes. Genome Res. 13:2052-2058.
9. Doebley, J. 2004. The genetics of maize evolution. Annu. Rev. Genet. 38:37-59.
10. Eyre-Walker, A., R. L. Gaut, H. Hilton, D. L. Feldman, and B. S. Gaut. 1998. Investigation of the bottleneck leading to the domestication of maize. Proc. Natl. Acad. Sci. USA 95:4441-4446.
11. Fay, J. C., and C. I. Wu. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413.
12. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
13. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
14. Fennoy, S. L., and J. Bailey-Serres. 1993. Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C and G-ending codons. Nucleic Acids Res. 21:5294-5300.
15. Filatov, D. A. 2002. ProSeq: a software for preparation and evolutionary analysis of DNA sequence data sets. Mol. Ecol. Notes 2:621-624.
16. Force, A., M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan, and J. Postlethwait. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
17. Fu, H., Z. Zheng, and H. K. Dooner. 2002. Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. USA 99:1082-1087.
18. Gaut, B. S., and J. F. Doebley. 1997. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 94:6809-6814.
19. Goldman, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
20. Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
21. Goloubinoff, P., S. Pääbo, and A. C. Wilson. 1993. Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens. Proc. Natl. Acad. Sci. USA 90:1997-2001.
22. Higo, K., Y. Ugawa, M. Iwamoto, and T. Korenaga. 1999. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic acids Res. 27:297-300.
23. Hileman, L. C., and D. A. Baum. 2003. Why do paralogs persist? Molecular evolution of CYCLOIDEA and related floral symmetry genes in Antirrhineae (Veronicaceae). Mol. Biol. Evol. 20:591-600.
24. Hofer, J., L. Turner, R. Hellens, M. Ambrose, P. Matthews, A. Michael, and N. Ellis. 1997. UNIFOLIATA regulates leaf and flower morphogenesis in pea. Curr. Biol. 7:581-587.
25. Hong, R. L., L. Hamaguchi, M. A. Busch, and D. Weigel. 2003. Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing. Plant Cell 15:1296-1309.
26. Hudson, R. R. M., M. Kreitman, and M. Aguadé. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
27. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
28. Kaplinsky, N. J., D. M. Braun, J. Penterman, S. A. Goff, and M. Freeling. 2002. Utility and distribution of conserved noncoding sequences in the grasses. Proc. Natl. Acad. Sci. USA 99:6147-6151.
29. Kellogg, E. A. 2000. Molecular and morphological evolution in Andropogoneae. Pp. 149-158 in S. W. L. Jacobs and J. E. Everett, eds. Grasses: systematics and evolution. Commonwealth Scientific and Industrial Research Organization (CSIRO), Collingwood, Victoria, Australia.
30. Koch, M. A., B. Weisshaar, J. Kroymann, B. Haubold, and T. Mitchell-Olds. 2001. Comparative genomics and regulatory evolution: conservation and function of the Chs and Apetala3 promoters. Mol. Biol. Evol. 18:1882-1891.
31. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
32. Kyozuka, J., S. Konishi, K. Nemoto, T. Izawa, and K. Shimamoto. 1998. Down-regulation of RFL, the FLO/LFY homolog of rice, accompanied with panicle branch initiation. Proc. Natl. Acad. Sci. USA 95:1979-1982.
33. Levy, S., S. Hannenhalli, and C. Workman. 2001. Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics 17:871-877.
34. Lukens, L., and J. F. Doebley. 2001. Molecular evolution of the teosinte branched 1 gene among maize and related grasses. Mol. Biol. Evol. 18:627-638.
35. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
36. Mathews, S., R. E. Spangler, R. J. Mason-Gamer, and E. A. Kellogg. 2002. Phylogeny of Andropogoneae inferred from Phytochrome B, GBSSI, and ndhf. Int. J. Plant Sci. 163:441-450.
37. Molinero-Rosales, N., M. Jamilena, S. Zurita, P. Gomez, J. Capel, and R. Lozano. 1999. FALSIFLORA, the tomato orthologue of FLORICAULA and LEAFY, controls flowering time and floral meristem identity. Plant J. 20:685-693.
38. Montero, L. M., J. Salinas, G. Matassi, and G. Bernardi. 1990. Gene distribution and isochore organization in the nuclear genome of plants. Nucleic Acids Res. 18:1859-1867.
39. Nielsen, R., and Z. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
40. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, Heidelberg, Germany.
41. Page, R. D. M. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:357-358.
42. Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
43. Prasad, K., K. Kushalappa, and U. Vijayraghavan. 2003. Mechanism underlying regulated expression of RFL, a conserved transcription factor, in the developing rice inflorescence. Mech. Dev. 120:491-502.
44. Purvis, I. J., A. J. Bettany, T. C. Santiago, J. R. Coggins, K. Duncan, R. Eason, and A. J. Brown. 1987. The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis. J. Mol. Biol. 193:413-417.
45. Rambaut, A. 1996. Se-Al: sequence alignment editor. (http://evolve.zoo. ox.ac.uk/).
46. Reidt, W., T. Wohlfarth, M. Ellerstrom, A. Czihal, A. Tewes, I. Ezcurra, L. Rask, and H. Baumlein. 2000. Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product. Plant J. 21:401-408.
47. Remington, D. L., J. M. Thornsberry, Y. Matsuoka, L. M. Wilson, S. R. Whitt, J. Doebley, S. Kresovich, M. M. Goodman, and E. S. Buckler IV. 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. USA 98:11479-11484.
48. Rozas, J., J. C. Sanchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
49. Salinas, J., G. Matassi, L. M. Montera, and G. Bernardi. 1988. Compositional compartmentalization and compositional patterns in the nuclear genomes of plants. Nucleic Acids Res. 16:4269-4285.
50. Schaal, T. D., and T. Maniatis. 1999. Selection and characterization of pre-mRNA splicing enhancers: identification of novel SR protein-specific enhancer sequences. Mol. Cell. Biol. 19:1705-1719.
51. Schug, J., and G. C. Overton. 1997. TESS: transcription element search software on the WWW. Technical report CBIL-TR-1997-1001-v0.0. Computational Biology and Informatics Laboratory, School of Medicine, University of Pennsylvania, Philadelphia, Pa.
52. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
53. Shu, G., W. Amaral, L. C. Hileman, and D. A. Baum. 2000. LEAFY and the evolution of rosette flowering in violet cress (Jonopsidium acaule, Brassicaceae). Am. J. Bot. 87: 634-641.
54. Simonsen, K. L., G. A. Churchill, and C. A. Aquadro. 1995. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141:413-429.
55. Souer, E., A. van der Krol, D. Kloos, C. Spelt, M. Bliek, J. Mol, and R. Koes. 1998. Genetic control of branching pattern and floral identity during Petunia inflorescence development. Development 125:733-742.
56. Spangler, R., B. Zaitchik, E. Russo, and E. Kellogg. 1999. Andropogoneae evolution and generic limits in Sorghum (Poaceae) using ndhf sequences. Syst. Bot. 24:267-281.
57. Swofford, D. L. 2003. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
58. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
59. Tajima, F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599-607.
60. Talbert, L. E., J. F. Doebley, S. R. Larson, and V. L. Chandler. 1990. Tripsacum andersonii is a natural hybrid involving Zea and Tripsacum: molecular evidence. Am. J. Bot. 77: 722-726.
61. Tavaré, S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lect. Math. Life Sci. 17:57-86.
62. Tenaillon, M. I., M. C. Sawkins, A. D. Long, R. L. Gaut, J. F. Doebley, and B. S. Gaut. 2001. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. USA 98:9161-9166.
63. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
64. Tiffin, P., and B. S. Gaut. 2001. Sequence diversity in the tetraploid Zea perennis and the closely related diploid Z. diploperennis: insights from four nuclear loci. Genetics 158:401-412.
65. Van de Peer, Y., J. S. Taylor, I. Braasch, and A. Meyer. 2001. The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J. Mol. Evol. 53:436-446.
66. Wall, J. D. 1999. Recombination and the power of statistical tests of neutrality. Genet. Res. 74:65-79.
67. Wang, R. L., A. Stec, J. Hey, L. Lukens, and J. Doebley. 1999. The limits of selection during maize domestication. Nature 398: 236-239.
68. Wang, Y., W. Devereux, T. M. Stewart, and R. A. Casero Jr. 2001. Characterization of the interaction between the transcription factors human polyamine modulated factor (PMF-1) and NF-E2-related factor 2 (Nrf-2) in the transcriptional regulation of the spermidine/spermine N1-acetyltransferase (SSAT) gene. Biochem. J. 355:45-49.
69. Weigel, D., J. Alvarez, D. R. Smyth, M. F. Yanofsky, and E. M. Meyerowitz. 1992. LEAFY controls floral meristem identity in Arabidopsis. Cell 69:843-859.
70. White, S. E., and J. F. Doebley. 1999. The molecular evolution of terminal earl, a regulatory gene in the genus Zea. Genetics 153:1455-1462.
71. Wright, F. 1990. The 'effective number of codons' used in a gene. Gene 87:23-29.
72. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13:555-556.
73. Yang, Z. 1998. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
74. Yang, Z., R. Nielsen, N. Goldman, and A. M. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
75. Yoon, H. S., and D. Baum. 2004. Transgenic study of parallelism in plant morphological evolution. Proc. Natl. Acad. Sci. USA. 101:6524-6529.
76. Zhang, L., S. Kosakovsky Pond, and B. S. Gaut. 2001. A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa. J. Mol. Evol. 52:144-156.
77. Zhu, B. Y., N. E. Zhou, C. M. Kay, and R. S. Hodges. 1993. Packing and hydrophobicity effects on protein folding and stability: effects of beta-branched amino acids, valine and isoleucine, on the formation and stability of two-stranded alpha-helical coiled coils/leucine zippers. Protein Sci. 2:383-394.