Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.

Abstract

The MIKC MADS-box gene family has been shaped by extensive gene duplications giving rise to subfamilies of genes with distinct functions and expression patterns. However, within these subfamilies the functional assignment is not that clear-cut, and considerable functional redundancy exists. One way to investigate the diversity in regulation present in these subfamilies is promoter sequence analysis. With the advent of genome sequencing projects, we are now able to exert a comparative analysis of Arabidopsis and poplar promoters of MADS-box genes belonging to the same subfamily. Based on the principle of phylogenetic footprinting, sequences conserved between the promoters of homologous genes are thought to be functional. Here, we have investigated the evolution of MADS-box genes at the promoter level and show that many genes have diverged in their regulatory sequences after duplication and/or speciation. Furthermore, using phylogenetic footprinting, a distinction can be made between redundancy, neo/nonfunctionalization, and subfunctionalization.

Supplementary Data

• Table S1: Motif occurrence in randomized datasets.
• Table S2: Number of motifs of a certain size in one-to-one subfamilies.
• Table S3: Number of motifs of a certain size in two-to-one subfamilies, no losses allowed.
• Table S4: Number of motifs of a certain size in two-to-one subfamilies, losses allowed.
• Table S5: Number of motifs of a certain size in 'many' subfamilies, no losses allowed.
• Table S6: Number of motifs of a certain size in 'many' subfamilies, losses allowed.
• Table S7: Summary of comparison between FootPrinter motifs and motifs from public databases.
• Fig. S1: Motifs detected through FootPrinter in the promoters of one-to-one Arabidopsis and poplar MADS-box genes.
• Fig. S2: Motifs detected through FootPrinter in the promoters of two-to-one Arabidopsis and poplar MADS-box genes.
• Fig. S3: Motifs detected through FootPrinter in the promoters of 'many'
• Fig. S4: Motifs detected through FootPrinter in the promoters of Arabidopsis and poplar AP3 homologs.
• Protein sequences of Poplar MADS-box genes used in this analysis.

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