MBE Advance Access originally published online on August 29, 2003
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Mol. Biol. Evol. 20(12):1963-1977. 2003
DOI: 10.1093/molbev/msg216
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Evolution and Divergence of the MADS-Box Gene Family Based on Genome-Wide Expression Analyses
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* Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
National Institute for Basic Biology, Okazaki, Japan
Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
Department of Molecular Biomechanics, The Graduate University for Advanced Studies, Okazaki, Japan
E-mail: mhasebe{at}nibb.ac.jp.
MADS-box genes encode transcription factors involved in various important aspects of development and differentiation in land plants, metazoans, and other organisms. Three types of land plant MADS-box genes have been reported. MIKCC- and MIKC*-type genes both contain conserved MADS and K domains but have different exon/intron structures. M-type genes lack a K domain. Most MADS-box genes previously analyzed in land plants are expressed in the sporophyte (diploid plant body); few are expressed in the gametophyte (haploid plant body). Land plants are believed to have evolved from a gametophyte (haploid)-dominant ancestor without a multicellular sporophyte (diploid plant body); most genes expressed in the sporophyte probably originated from those used in the gametophyte during the evolution of land plants. To analyze the evolution and diversification of MADS-box genes in land plants, gametophytic MADS-box genes were screened using macroarray analyses for 105 MADS-box genes found in the Arabidopsis genome. Eight MADS-box genes were predominantly expressed in pollen, the male gametophyte; all but one of their expression patterns was confirmed by Northern analyses. Analyses of the exon/intron structure of these seven genes revealed that they included two MIKCC-type, one M-type, and four MIKC*-type MADS-box genes. Previously, MIKC*-type genes have been reported only from a moss and a club moss, and this is the first record in seed plants. These genes can be used to investigate the unknown ancestral functions of MADS-box genes in land plants. The macroarray analyses did not detect expression of 56 of 61 M-type MADS-box genes in any tissues examined. A phylogenetic tree including all three types of Arabidopsis MADS-box genes with representative genes from other organisms showed that M-type genes were polyphyletic and that their branch lengths were much longer than for the other genes. This finding suggests that most M-type genes are pseudogenes, although further experiments are necessary to confirm this possibility. Our global phylogenetic analyses of MADS-box genes did not support the previous classification of MADS-box genes into type I and II groups, based on smaller scale analyses. An evolutionary scenario for the evolution of MADS-box genes in land plants is discussed.
Key Words: MADS-box • Arabidopsis • genome • gene family • sporophyte • gametophyte
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