MADS-box genes

Some references for MADS-box genes

Abascal, F., R. Zardoya, et al. (2005). "ProtTest: selection of best-fit models of protein evolution." Bioinformatics 21(9): 2104-5.

Alvarez-Buylla, E. R., S. J. Liljegren, et al. (2000). "MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes." Plant J 24(4): 457-66.

Alvarez-Buylla, E. R., S. Pelaz, et al. (2000). "An ancestral MADS-box gene duplication occurred before the divergence of plants and animals." Proc Natl Acad Sci U S A 97(10): 5328-33.

Becker, A. and G. Theissen (2003). "The major clades of MADS-box genes and their role in the development and evolution of flowering plants." Mol Phylogenet Evol 29(3): 464-89.

Black, D. L. (2003). "Mechanisms of alternative pre-messenger RNA splicing." Annu Rev Biochem 72: 291-336.

Causier, B., R. Castillo, et al. (2005). "Evolution in action: following function in duplicated floral homeotic genes." Curr Biol 15(16): 1508-12.

Chen, F. C., S. S. Wang, et al. (2007). "Plant gene and alternatively spliced variant annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species." Plant Physiology 143(3): 1086-1095.

Cseke, L. and G. Podila (2004). "MADS-box genes in dioecious aspen II: a review of MADS-box genes from trees and their potential in forest biotechnology." Physiology and Molecular Biology of Plants 10(1): 7-28.

de Folter, S., R. G. Immink, et al. (2005). "Comprehensive interaction map of the Arabidopsis MADS Box transcription factors." Plant Cell 17(5): 1424-33.

Egea-Cortines, M., H. Saedler, et al. (1999). "Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus." Embo J 18(19): 5370-9.

Glazko, G. V. and M. Nei (2003). "Estimation of divergence times for major lineages of primate species." Mol Biol Evol 20(3): 424-34.

Guindon, S. and O. Gascuel (2003). "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood." Syst Biol 52(5): 696-704.

Guindon, S., F. Lethiec, et al. (2005). "PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference." Nucleic Acids Res 33(Web Server issue): W557-9.

Hartmann, U., S. Hohmann, et al. (2000). "Molecular cloning of SVP: a negative regulator of the floral transition in Arabidopsis." Plant J 21(4): 351-60.

Hartwell, L., L. Hood, et al. (2004). Genetics: from genes to genomes, McGraw-Hill Higher Education, Boston.

Hernandez-Hernandez, T., L. P. Martinez-Castilla, et al. (2007). "Functional diversification of B MADS-box homeotic regulators of flower development: Adaptive evolution in protein-protein interaction domains after major gene duplication events." Mol Biol Evol 24(2): 465-81.

Hileman, L. C., J. F. Sundstrom, et al. (2006). "Molecular and phylogenetic analyses of the MADS-box gene family in tomato." Mol Biol Evol 23(11): 2245-58.

Honma, T. and K. Goto (2001). "Complexes of MADS-box proteins are sufficient to convert leaves into floral organs." Nature 409(6819): 525-9.

Irish, V. F. and A. Litt (2005). "Flower development and evolution: gene duplication, diversification and redeployment." Curr Opin Genet Dev 15(4): 454-60.

Katoh, K., K. Kuma, et al. (2005). "MAFFT version 5: improvement in accuracy of multiple sequence alignment." Nucleic Acids Res 33(2): 511-8.

Katoh, K., K. Misawa, et al. (2002). "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform." Nucleic Acids Res 30(14): 3059-66.

Kaufmann, K., R. Melzer, et al. (2005). "MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants." Gene 347(2): 183-98.

Kramer, E. M., M. A. Jaramillo, et al. (2004). "Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms." Genetics 166(2): 1011-23.

Krizek, B. A. and J. C. Fletcher (2005). "Molecular mechanisms of flower development: an armchair guide." Nat Rev Genet 6(9): 688-98.

Litt, A. and V. F. Irish (2003). "Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development." Genetics 165(2): 821-33.

Moore, R. C. and M. D. Purugganan (2005). "The evolutionary dynamics of plant duplicate genes." Curr Opin Plant Biol 8(2): 122-8.

Nam, J., C. W. dePamphilis, et al. (2003). "Antiquity and evolution of the MADS-box gene family controlling flower development in plants." Mol Biol Evol 20(9): 1435-47.

Nam, J., J. Kim, et al. (2004). "Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms." Proc Natl Acad Sci U S A 101(7): 1910-5.

Ng, M. and M. F. Yanofsky (2001). "Function and evolution of the plant MADS-box gene family." Nat Rev Genet 2(3): 186-95.

Parenicova, L., S. de Folter, et al. (2003). "Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world." Plant Cell 15(7): 1538-51.

Posada, D. and T. R. Buckley (2004). "Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests." Syst Biol 53(5): 793-808.

Posada, D. and K. A. Crandall (1998). "MODELTEST: testing the model of DNA substitution." Bioinformatics 14(9): 817-8.

Promega (2005). ImProm-II reverse transcription system.

QIAGEN (2001). RNeasy Mini Handbook, QIAGEN Inc.

Ratcliffe, O. J., R. W. Kumimoto, et al. (2003). "Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold." Plant Cell 15(5): 1159-69.

Reddy, A. S. N. (2007). "Alternative splicing of pre-messenger RNAs in plants in the genomic era." Annual Review of Plant Biology 58: 267-294.

Rijpkema, A. S., T. Gerats, et al. (2007). "Evolutionary complexity of MADS complexes." Curr Opin Plant Biol 10(1): 32-8.

Sablowski, R. W. and E. M. Meyerowitz (1998). "Temperature-sensitive splicing in the floral homeotic mutant apetala3-1." Plant Cell 10(9): 1453-63.

Sheldon, C. C., A. B. Conn, et al. (2002). "Different regulatory regions are required for the vernalization-induced repression of FLOWERING LOCUS C and for the epigenetic maintenance of repression." Plant Cell 14(10): 2527-37.

Sheldon, C. C., D. T. Rouse, et al. (2000). "The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC)." Proc Natl Acad Sci U S A 97(7): 3753-8.

Theissen, G. (2001). "Development of floral organ identity: stories from the MADS house." Curr Opin Plant Biol 4(1): 75-85.

Theissen, G., A. Becker, et al. (2000). "A short history of MADS-box genes in plants." Plant Mol Biol 42(1): 115-49.

Theissen, G. and H. Saedler (2001). "Plant biology. Floral quartets." Nature 409(6819): 469-71.

Tuskan, G. A., S. Difazio, et al. (2006). "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)." Science 313(5793): 1596-604.

Tzeng, T. Y., H. C. Liu, et al. (2004). "The C-terminal sequence of LMADS1 is essential for the formation of homodimers for B function proteins." J Biol Chem 279(11): 10747-55.

Vandenbussche, M., G. Theissen, et al. (2003). "Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations." Nucleic Acids Res 31(15): 4401-9.

Wang, B. B. and V. Brendel (2006). "Genomewide comparative analysis of alternative splicing in plants." Proc Natl Acad Sci U S A 103(18): 7175-80.

Wernersson, R. and A. G. Pedersen (2003). "RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences." Nucleic Acids Res 31(13): 3537-9.

Zhu, Q. H., A. Y. Guo, et al. (2007). "DPTF: a database of poplar transcription factors." Bioinformatics 23(10): 1307-8.