|
1. Alexander, D., Goodman, R.M., Gut-Rella, M., Glascock, C., Weymann, K., Friedrich, L., Maddox, D., Ahl-Goy, P., Luntz, T., Ward, E., et al. (1993). Increased tolerance to two oomycete pathogens in transgenic tobacco expressing pathogenesis-related protein 1a. Proc Natl Acad Sci U S A 90, 7327-7331.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generate of protein database search programs. Nucleic Acid Research 25, 3389-3402.
3. Arabidopsis_Genome_Initiative. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
4. Banuelos, M.A., Garciadeblas, B., Cubero, B., and Rodriguez-Navarro, A. (2002). Inventory and functional characterization of the HAK potassium transporters of rice. Plant Physiol 130, 784-795.
5. Baumberger, N., Doesseger, B., Guyot, R., Diet, A., Parsons, R.L., Clark, M.A., Simmons, M.P., Bedinger, P., Goff, S.A., Ringli, C., et al. (2003). Whole-genome comparison of leucine-rich repeat extensins in Arabidopsis and rice. A conserved family of cell wall proteins form a vegetative and a reproductive clade. Plant Physiol 131, 1313-1326.
6. Baxter, I., Tchieu, J., Sussman, M.R., Boutry, M., Palmgren, M.G., Gribskov, M., Harper, J.F., and Axelsen, K.B. (2003). Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice. Plant Physiol 132, 618-628.
7. Becraft, P.W. (2002). Receptor kinase signaling in plant development. Annu Rev Cell Dev Biol 18, 163-192.
8. Becraft, P.W., Stinard, P.S., and McCarty, D.R. (1996). CRINKLY4: a TNFR-like receptor kinase involved in maize epidermal differentiation. Science 273, 1406-1409.
9. Blanc, G., Hokamp, K., and Wolfe, K.H. (2003). A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13, 137-144.
10. Bowers, J.E., Chapman, B.A., Rong, J., and Paterson, A.H. (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433-438.
11. Brand, U., Fletcher, J.C., Hobe, M., Meyerowitz, E.M., and Simon, R. (2000). Dependence of stem cell fate in Arabidopsis on a feedback loop regulated by CLV3 activity. Science 289, 617-619.
12. Canales, C., Bhatt, A.M., Scott, R., and Dickinson, H. (2002). EXS, a putative LRR receptor kinase, regulates male germline cell number and tapetal identity and promotes seed development in Arabidopsis. Curr Biol 12, 1718-1727.
13. Chaw, S.-M., Chang, C.-C., Chen, H.-L., and Li, W.-H. (2003). Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol, (in press).
14. Clark, S.E., Williams, R.W., and Meyerowitz, E.M. (1997). The CLAVATA1 gene encodes a putative receptor kinase hat controls shoot and floral meristem size in Arabidopsis. Cell 89, 575-585.
15. Comeron, J.M. 1995. A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J. Mol. Evol. 41:1152-1159
16. Dievart, A. and Clark, S.E. (2003). Using mutant alleles to determine the structure and function of leucine-rich repeat receptor-like kinases. Curr Opin Plant Biol 6, 507-516.
17. Doebley, J. and Lukens, L. (1998). Transcriptional regulators and the evolution of plant form. Plant Cell 10, 1075-1082.
18. Endre, G., Kereszt, A., Kevei, Z., Mihacea, S., Kalo, P., and Kiss, G.B. (2002). A receptor kinase gene regulating symbiotic nodule development. Nature 417, 962-966.
19. Feuillet, C., Schachermayr, G., and Keller, B. (1997). Molecular cloning of a new receptor-like kinase gene encoded at the Lr10 disease resistance locus of wheat. Plant J. 11, 45-52.
20. Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92-100.
21. Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequence. Mol. Biol. Evol. 11:725-736.
22. Gomez-Gomez, L. and Boller, T. (2000). FLS2: an LRR receptor-like kinase invovled in the perception of bacterial elicitor flagellin in Arabidopsis. Mol. Cell 5, 1003-1011.
23. Goremykin, V.V., Hansmann, S., and Martin, W.F. (1997). Evolutionary analysis of 58 proteins encoded in six completely sequenced chloroplast genomes: revised molecular estimates of two seed plant divergence times. Plant Syst Evol 206, 337-351.
24. Hanks, S.K. and Hunter, T. (1995). The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FAESB J. 9, 576-596.
25. Hardie, D.G. (1999). Plant protein serine/threonine kinases: classification and functions. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50, 97-131.
26. He, Z., Wang, Z.Y., Li, J., Zhu, Q., Lamb, C., Ronald, P., and Chory, J. (2000). Perception of barssinosteroids by the extracellular domain of the receptor kinase BRI1. Science 288, 2360-2363.
27. He, Z.-H., He, D., and Kohorn, B.D. (1998). Requirement for the induced expression of a cell wall associated receptor kinase for survival during the pathogen response. Plant J. 14.
28. Hecht, V., Vielle-Calzada, J.P., Hartog, M.V., Schmidt, E.D., Boutilier, K., Grossniklaus, U., and de Vries, S.C. (2001). The Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASE 1 gene is expressed in developing ovules and embryos and enhances embryogenic competence in culture. Plant Physiol 127, 803-816.
29. Higgins, D.G., Thompson, J.D., and Gibson, T.J. (1996). Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266, 383-402.
30. Holmquiat, R. and D. Pearl. 1980. Theoretical foundations for quantitative paleogenetics III. The molecular divergence of nucleic acids and proteins for the case of genetic events of unequal probability. J. Mol. Evol. 16: 211-267.
31. Huke, R.E. and Huke, E.H. (1990). Rice: Then and Now. (Manila: International Rice Research Institute).
32. Hunter, T. and Plowman, G.D. (1997). The protein kinases of budding yeast: six score and more. Trends Biochem Sci 22, 18-22.
33. Ina, Y. 1995. New methods for estimating the numbers of synonymous andnonsynonymous substitutions. J. Mol. Evol. 40:190-226.
34. Jasinski, M., Ducos, E., Martinoia, E., and Boutry, M. (2003). The ATP-binding cassette transporters: structure, function, and gene family comparison between rice and Arabidopsis. Plant Physiol 131, 1169-1177.
35. Jinn, T.L., Stone, J.M., and Walker, J.C. (2000). HAESA, an Arabidopsis leucine-rich repeat receptor kinase, controls floral organ abscission. Gene Dev. 14, 108-117.
36. Jukes, KH., and CR. Cantor. 1969. Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21-132.
37. Kaplan, N. L. and K. Risko. 1982. A method for estimating rates of nucleotide substitution using DNA sequence data. Theor. Pop. Biol. 21:318-328.
38. Karlowski, W.M., Schoof, H., Janakiraman, V., Stuempflen, V., and Mayer, K.F. (2003). MOsDB: an integrated information resource for rice genomics. Nucleic Acids Res 31, 190-192.
39. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
40. Kimura, M. 1981. Estimation of evolutionary distance between homologous nucleotide sequence. Proc. Natl. Acad. Sci. USA 78:454-458.
41. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England.
42. Kimura, M. and T. Ohta. 1972. On the stochastic model for estimation of mutational distance between homologous proteins. J. Mol. Evol. 2: 87-90.
43. Krusell, L., Madsen, L.H., Sato, S., Aubert, G., Genua, A., Szczyglowski, K., Duc, G., Kaneko, T., Tabata, S., de Bruijn, F., et al. (2002). Shoot control of root development and nodulation is mediated by a receptor-like kinase. Nature 420, 422-426.
44. Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20(1):86-93.
45. Lee, H.-S., Karunanandaa, B., McCubbin, A., Gilroy, S., and Kao, T.-H. (1996). PRK1, a receptor-like kinase of Petunia inflata, is essential for postmeiotic development of pollen. Plant J. 9, 613-624.
46. Lemaitre, B., Nicolas, E., Michaut, L., Reichhart, J.M., and Hoffmann, J.A. (1996). The dorsoventral regulatory gene cassette spatzle/Toll/cactus controls the potent antifungal response in Drosophila adults. Cell 86, 973-983.
47. Li, J. and Chory, J. (1997). A putative leucine-rich repeat receptor kinase involved in brassinosteroid signal transduction. 90 5.
48. Li, J., Wen, J., Lease, K.A., Doke, J.T., Tax, F.E., and Walker, J.C. (2002). BAK1, an Arabidopsis LRR receptor-like protein kinase, interacts with BRI1 and modulates brassinosteroid signaling. Cell 110, 213-222.
49. Li, W.-H. 1986. Evolutionary change of restriction cleavage sites and phylogenetic inference. Genetics 113: 187-213.
50. Li, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99.
51. Li, W.-H. 1997. Molecular evolution. Sinauer Associates, Sunderland, Mass.
52. Li, W.-H., C.-I. Wu, and C.-C. Luo. 1985. A new method for estimating synonymous and non-synonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.
53. Lijavetzky, D., Carbonero, P., and Vicente-Carbajosa, J. (2003). Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evol Biol 3, 17.
54. Limpens, E., Franken, C., Smit, P., Willemse, J., Bisseling, T., and Geurts, R. (2003). LysM Domain Receptor Kinases Regulating Rhizobial Nod Factor-Induced Infection. Science.
55. Madsen, E.B., Madsen, L.H., Radutoiu, S., Olbryt, M., Rakwalska, M., Szczyglowski, K., Sato, S., Kaneko, T., Tabata, S., Sandal, N., et al. (2003). A receptor kinase gene of the LysM type is involved in legumeperception of rhizobial signals. Nature 425, 637-640.
56. Manning, G., Whyte, D.B., Martinez, R., Hunter, T., and Sudarsanam, S. (2002). The protein kinase complement of the human genome. Science 298, 1912-1934.
57. Matsubayashi, Y., Ogawa, M., Morita, A., and Sakagami, Y. (2002). An LRR receptor kinase involved in perception of a peptide plant hormone, phytosulfokine. Science 296, 1470-1472.
58. Meyers, B.C., Shen, K.A., Rohani, P., Gaut, B.S., and Michelmore, R.W. (1998). Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection. Plant Cell 10, 1833-1846.
59. Meyers, B.C., Kozik, A., Griego, A., Kuang, H., and Michelmore, R.W. (2003). Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15, 809-834.
60. Michelmore, R.W. and Meyers, B.C. (1998). Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res 8, 1113-1130.
61. Miyata, T. and T. Yasunaga. 1980. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J. Mol. Evol. 16: 23-36.
62. Mondragon-Palomino, M., Meyers, B.C., Michelmore, R.W., and Gaut, B.S. (2002). Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res 12, 1305-1315.
63. Nam, K.H. and Li, J. (2002). BRI1/BAK1, a receptor kinase pair mediating brassinosteroid signaling. Cell 110, 203-212.
64. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
65. Nei, M., and S. Kumar. 2000. Molecular evolution and phylogenetics. Oxford University Press.
66. Nishimura, R., Hayashi, M., Wu, G.J., Kouchi, H., Imaizumi-Anraku, H., Murakami, Y., Kawasaki, S., Akao, S., Ohmori, M., Nagasawa, M., et al. (2002). HAR1 mediates systemic regulation of symbiotic organ development. Nature 420, 426-429.
67. Nurnberger, T. and Brunner, F. (2002). Innate immunity in plants and animals: emerging parallels between the recognition of general elicitors and pathogen-associated molecular patterns. Curr Opin Plant Biol 5, 318-324.
68. Ohtake, Y., Takahashi, T., and Komeda, Y. (2000). Salicylic acid induces the expression of a number of receptor-like kinase genes in Arabidopsis thaliana. Plant Cell Physiol. 41, 1038-1044.
69. O'Neill, L.A. (2002). Signal transduction pathways activated by the IL-1 receptor/toll-like receptor superfamily. Curr Top Microbiol Immunol 270, 47-61.
70. Pamilo, P., and N. O. Bianchi. 1993. Evolution of the Zfx and Zfy genes: Rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281.
71. Pastuglia, M., Roby, D., Dumas, C., and Cock, J.M. (1997). Rapid induction by wounding and bacterial infection of an S gene family receptor-like kinase gene in Brassica oleracea. Plant Cell 9, 49-60.
72. Plowman, G.D., Sudarsanam, S., Bingham, J., Whyte, D., and Hunter, T. (1999). The protein kinases of Caenorhabditis elegans: a model for signal transduction in multicellular organisms. Proc Natl Acad Sci U S A 96, 13603-13610.
73. Radutoiu, S., Madsen, L.H., Madsen, E.B., Felle, H.H., Umehara, Y., Gronlund, M., Sato, S., Nakamura, Y., Tabata, S., Sandal, N., et al. (2003). Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases. Nature 425, 585-592.
74. Robatzek, S. and Somssich, I.E. (2002). Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Genes Dev 16, 1139-1149.
75. Saitou, N. and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
76. Sanderson, M.J. (1997). A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol 14, 1218-1231.
77. Scheer, J.M. and Ryan, C.A., Jr. (2002). The systemin receptor SR160 from Lycopersicon peruvianum is a member of the LRR receptor kinase family. Proc Natl Acad Sci U S A 99, 9585-9590.
78. Schopfer, C., Nasrallah, M., and Nasrallah, J. (1999). The male determinane of self-incompatibility in Brassica. Science 286, 1697-1700.
79. Schultz, J., Copley, R.R., Doerks, T., Ponting, C.P., and Bork, P. (2000). SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acid Res. 28, 231-234.
80. Searle, I.R., Men, A.E., Laniya, T.S., Buzas, D.M., Iturbe-Ormaetxe, I., Carroll, B.J., and Gresshoff, P.M. (2003). Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science 299, 109-112.
81. Shelton, C.A. and Wasserman, S.A. (1993). Pelle encodes a protein kinase required to establish dorsoventral polarity in the Drosophila embryo. Cell 72, 515-525.
82. Shi, P., Zhang, J., Yang, H., and Zhang, Y.P. (2003). Adaptive diversification of bitter taste receptor genes in Mammalian evolution. Mol Biol Evol 20, 805-814.
83. Shiu, S.H. and Bleecker, A.B. (2001a). Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci U S A 98, 10763-10768.
84. Shiu, S.H. and Bleecker, A.B. (2001b). Plant receptor-like kinase gene family: diversity, function, and signaling. Sci STKE 2001, RE22.
85. Shiu, S.H. and Bleecker, A.B. (2003). Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis. Plant Physiol 132, 530-543.
86. Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF, Li WH. Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell. 2004 May;16(5):1220-34.
87. Shpak, E.D., Lakeman, M.B., and Torii, K.U. (2003). Dominant-negative receptor uncovers redundancy in the Arabidopsis ERECTA Leucine-rich repeat receptor-like kinase signaling pathway that regulates organ shape. Plant Cell 15, 1095-1110.
88. Silva, N.F. and Goring, D.R. (2002). The proline-rich, extensin-like receptor kinase-1 (PERK1) gene is rapidly induced by wounding. Plant Mol Biol 50, 667-685.
89. Simillion, C., Vandepoele, K., Van Montagu, M.C., Zabeau, M., and Van De Peer, Y. (2002). The hidden duplication past of Arabidopsisthaliana. Proc Natl Acad Sci U S A 99, 13627-13632.
90. Solovyev, V.V. (2002). Finding genes by computer: Probabilistic and discriminativeapproaches. In Current Topics in Computational Biology, T. Jiang, T. Smith, Y. Xu, and M. Zhang, eds (MIT Press), pp. 365-401.
91. Song, W.Y., Wang, G.L., Chen, L.L., Kim, H.S., Pi, L.Y., Holsten, T., Gadner, J., Wang, B., Zhai, W.X., Zhu, L.H., et al. (1995). A receptor kinase-like protein encoded by the rice disease resistance gene Xa21. Science 270.
92. Sonnhammer, E.L.L., Eddy, S.R., Birney, E., Bateman, A., and Durbin, R. (1998). Pfam: multiple seuqnce alignments and HMM-profiles of protein domains. Nucleic Acid Res. 26, 320-322.
93. Stracke, S., Kistner, C., Yoshida, S., Mulder, L., Sato, S., Kaneko, T., Tabata, S., Sandal, N., Stougaard, J., Szczyglowski, K., et al. (2002). A plant receptor-like kinase required for both bacterial and fungal symbiosis. Nature 417, 959-962.
94. Swiderski, M.R. and Innes, R.W. (2001). The Arabidopsis PBS1 resistance gene encodes a member of a novel protein kinase subfamily. Plant J 26, 101-112.
95. Torii, K.U. (2000). Receptor kinase activation and signal transduction in plants: an emerging picture. Curr. Opin. Plant Biol. 3, 361-367.
96. Torii, K.U., Mitsukawa, N., Oosumi, T., Matsuura, Y., Yokoyama, R., Whittier, R.F., and Komeda, Y. (1996). The Arabidopsis ERECTA gene encodes a putative receptor protein kinase with extracellular leucine-rich repeats. Plant Cell 8, 735-746.
97. Tzeng, Y.-H., Pan, R. and Li, W.-H. 2004. Comparison of Three Methods for Estimating Rates of Synonymous and Non-synonymous Nucleotide Substitutions. Mol. Biol. Evol. 21(12):2290–2298.
98. van der Geer, P., Hunter, T., and Lindberg, R.A. (1994). Receptor protein-tyrosine kinases and their signal transduction pathways. Annu Rev Cell Biol 10, 251-337.
99. Vandepoele, K., Simillion, C., and Van de Peer, Y. (2003). Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15, 2192-2202.
100. Vision, T.J., Brown, D.G., and Tanksley, S.D. (2000). The origins of genomic duplications in Arabidopsis. Science 290, 2114-2117.
101. Walker, J.C. and Zhang, R. (1990). Relationship of a putative receptor protein kinase from maize to the S-locus glycoproteins of Brassica. Nature 345, 743-746.
102. Wikstrom, N., Savolainen, V., and Chase, M.W. (2001). Evolution of the angiosperms: calibrating the family tree. Proc R Soc Lond B Biol Sci 268, 2211-2220.
103. Wolfe, K.H., Gouy, M., Yang, Y.W., Sharp, P.M., and Li, W.H. (1989). Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci U S A 86, 6201-6205.
104. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
105. Young, J.M., Friedman, C., Williams, E.M., Ross, J.A., Tonnes-Priddy, L., and Trask, B.J. (2002). Different evolutionary processes shaped the mouse and human olfactory receptor gene families. Hum Mol Genet 11, 535-546.
106. Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79-92.
107. Zhao, D.Z., Wang, G.F., Speal, B., and Ma, H. (2002). The excess microsporocytes1 gene encodes a putative leucine-rich repeat receptor protein kinase that controls somatic and reproductive cell fates in the Arabidopsis anther. Genes Dev 16, 2021-2031.
108. Zharkikh, A. 1994. Estimation of evolutionary distances between nucleotide sequences. J. Mol. Evol. 39:315-329.
|