Molecular Evolution of the Phytochrome Gene Family in Sorghum: Changing Rates of Synonymous and Replacement Evolution

Molecular Biology and Evolution

Volumn 21, Issue 4, 2004, Pages 716-723

  White, Gemma M ^a   Hamblin, Martha T ^b   Kresovich, Stephen ^b  

^a Inst Arable Crops Res Rothamsted   (United Kingdom)

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

Author keywords

Evolution; Phytochrome; Polymorphism; Population genetics; Selection; Sorghum

Indexed keywords

DNA; PHYTOCHROME;

AMINO ACID SEQUENCE; ARTICLE; DNA SEQUENCE; GENE LOCUS; GENETIC POLYMORPHISM; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTORECEPTOR; PLANT; POLYMERASE CHAIN REACTION; POPULATION GENETICS; SORGHUM; SPECIES DIFFERENTIATION;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BASE SEQUENCE; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYTOCHROME; POLYMORPHISM, GENETIC; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SORGHUM;

EMBRYOPHYTA; SORGHUM BICOLOR;

EID: 1842557439     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh067     Document Type: Article

References (38)

1. Alba, R., P. M. Kelmenson, M. M. Cordonnier-Pratt, and L. H. Pratt. 2000. The phylochrome gene family in tomato and the rapid differential evolution of this family in angiosperms. Mol. Biol. Evol. 17:362-373.
2. Aldrich, P. R., and J. Doebley. 1992. Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorgbum bicolor. Theor. Appl. Genet. 85:293-302.
3. Aldrich, P. R., J. Doebley, K. F. Schertz, and A. Stec. 1992. Patterns of allozyme variation in cultivated and wild Sorghum bicolor. Theor. Appl. Genet. 85:451-460.
4. Childs, K. L., F. R. Miller, M. M. Cordonnier-Pratt, L. H. Pratt, P. W. Morgan, and J. E. Mullet. 1997. The sorghum photoperiod sensitivity gene, Ma3, encodes a phytochrome B. Plant Physiol. 113:611-619.
5. Clack, T., S. Mathews, and R. A. Sharrock. 1994. The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE. Plant Mol. Biol. 25:413-427.
6. Cui, Y. X., G. W. Xu, C. W. Magill, K. F. Schertz, and G. E. Hart. 1995. RFLP-based assay of Sorghum bicolor (L.) Moench genetic diversity. Theor. Appl. Genet. 90:787-796.
7. Devlin, P. F., D. E. Somers, P. H. Quail, and G. C. Whitelam. 1997. The Brassica rapa elongated intemode (EIN) gene encodes phytochrome B. Plant Mol. Biol. 34:537-547.
8. Doyle, J. J., and J. L. Doyle. 1987. A rapid DNA isolation procedure for small amounts of leaf tissue. Phytochem. Bull. 19:11-15.
9. DuMont, N., V. Bauer, J. C. Fay, P. P. Calabrese and C. F. Aquandro. 2004. DNA variability and divergence at the Notch locus region of Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence. Genetics (in press).
10. García-Gil, M. R., M. Mikkonen, and O. Savolainen. 2003. Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Mol. Ecol. 12:1195-1206.
11. Gaut, B. S., and J. Doebley. 1997. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 94:6809-6814.
12. Hamblin, M. T., S. E. Mitchell, G. M. White, J. Gallego, R. Kukatla, R. A. Wing, A. H. Paterson, and S. Kresovich. 2004. Comparative population genetics of the panicoid grasses: Sequence polymorphism, linkage disequilibrium, and selection in a diverse sample of Sorghum bicolor. Genetics (in press).
13. Hilton, H., and B. S. Gaut. 1998. Speciation and domestication in maize and its wild relatives: evidence from the globulin-1 gene. Genetics 150:863-872.
14. Howe, G. T., P. A. Bucciaglia, W. P. Hackett, G. R. Furnier, M. M. Cordonnier-Pratt, and G. Gardner. 1998. Evidence that the phytochrome gene family in black cottonwood has one PHYA locus and two PHYB loci but lacks members of the PHYC/F and PHYE subfamilies. Mol. Biol. Evol. 15:160-175.
15. Hudson, R. R., M. Kreitman, and M. Aguade. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
16. Kimber, C. 2000. Origins of domesticated sorghum and its early diffusion to India and China. Pp. 3-98 in W. C. Smith and R. A. Frederiksen, eds. Sorghum. John Wiley, New York.
17. Kolukisaoglu, H. U., S. Marx, C. Wiegmann, S. Hanelt, and H. A. Schneider-Poetsch. 1995. Divergence of the phytochrome gene family predates angiosperm evolution and suggests that Selaginella and Equisetum arose prior to Psilotum. J. Mol. Evol. 41:329-337.
18. Koomneef, M., C. Alonso-Blanco, A. J. M. Peeters, and W. Soppe. 1998. Genetic control of flowering time in Ambidopsis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49:345-370.
19. Mathews, S., J. G. Burleigh, and M. J. Donoghue. 2003. Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms. Mol. Biol. Evol. 20:1087-1097.
20. Mathews, S., and M. J. Donoghue. 2000. Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. Int. J. Plant Sci. 161:S41-S55.
21. Mathews, S., M. Lavin, and R. A. Sharrock. 1995. Evolution of the phytochrome gene family and its utility for phylogenetic analyses of angiosperms. Ann. Missouri Bot. Garden 82:296-321.
22. Mathews, S., and R. A. Sharrock. 1996. The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms. Mol. Biol. Evol. 13:1141-1150.
23. -. 1997. Phytochrome gene diversity. Plant, Cell Environ. 20:666-671.
24. McDonald, J. H., and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
25. Miyashita, N. T., A. Kawabe, H. Innan, R. Terauch. 1998. Intra- and interspecific DNA variation and codon bias of the alcohol dehydrogenase (Adh) locus in Arabis and Arabidopsis species. Mol. Biol. Evol. 15:1420-1429.
26. Monte, E., J. M. Alonso, J. R. Ecker, Y. Zhang, X. Li, J. Young, S. Austin-Phillips, and P. H. Quail. 2003. Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. Plant Cell 15:1962-1980.
27. Morgan, P. W., S. A. Finlayson, K. L. Childs, J. E. Mullet, and W. L. Rooney. 2002. Opportunities to improve adaptability and yield in grasses: lessons from sorghum. Crop Sci. 42:1791-1799.
28. Nagatani, A., J. W. Reed, and J. Chory. 1993. Isolation and initial characterization of Arabidopsis mutants that are deficient in phytochrome A. Plant Physiol. 102:269-277.
29. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
30. Reed, J. W., A. Nagatani, T. D. Elich, M. Fagan, and J. Chory. 1994. Phytochrome A and phytochrome B have overlapping but distinct functions in Arabidopsis development. Plant Physiol 104:1139-1149.
31. Rozas, J., and R. Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
32. Smith, H. 2000. Phytochromes and light signal perception by plants-an emerging synthesis. Nature 407:585-591.
33. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
34. Weinig, C., M. C. Ungerer, L. A. Dorn, N. C. Kane, Y. Toyonaga, S. S. Halldorsdottir, T. F. Mackay, M. D. Purugganan, and J. Schmitt. 2002. Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments. Genetics 162:1875-1884.
35. Weller, J. L., M. E. Schreuder, H. Smith, M. Koomneef, and R. E. Kendrick. 2000. Physiological interactions of phytochromes A, B1 and B2 in the control of development in tomato. Plant J. 24:345-356.
36. White, S. E., and J. F. Doebley. 1999. The molecular evolution of terminal ear1, a regulatory gene in the genus Zea. Genetics 153:1455-1462.
37. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13:555-556.
38. Yang, Z., and R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917.