Fig. 1. Unrooted maximum-likelihood tree of the AP2/EREBP multigene family. All Arabidopsis thaliana genes of the AP2/EREBP multigene family were used. Local bootstrap probabilities are shown on or below branches. Scale bar corresponds to 0.1 amino acid substitutions per residue. Two AP2 domains of the AP2 subfamily genes, the AP2 repeat-1 domain and the AP2 repeat-2 domain, were treated separately as two OTUs. In the AP2 subfamily, R1 indicates the AP2 repeat-1 domain, and R2 indicates the AP2 repeat-2 domain.

Fig. 2. Maximum-likelihood tree of the AP2 subfamily using separated AP2 domains. We used 60 amino acid residues of the AP2/ERF domain region. Local bootstrap probabilities are shown on or below the main branches of the tree. Scale bar corresponds to 0.1 amino acid substitutions per residue. We used the genes isolated in this study and all genes of Arabidopsis thaliana, Antirrhinum majus, Brassica napus, Petunia hybrida, Oryza sativa, Zea mays, and Picea abies that were registered in the NCBI database in November 2003 as well as Chlamydomonas reinhardtii AV622151. The A. thaliana RAV group was used as the outgroup. Two AP2 domains of the AP2 subfamily genes, the AP2 repeat-1 domain and the AP2 repeat-2 domain, were treated separately as two OTUs. In the AP2 subfamily, R1 indicates the AP2 repeat-1 domain, and R2 indicates the AP2 repeat-2 domain.

Fig. 3. Maximum-likelihood tree of the AP2 subfamily using the AP2 domain-linker region. We used 86 amino acid residues of the AP2 domain-linker region of the AP2 subfamily genes. Local bootstrap probabilities are shown on or below the branches. Scale bar corresponds to 0.01 amino acid substitution per residue. We used the genes isolated in this study and all genes of Arabidopsis thaliana, Antirrhinum majus, Brassica napus, Malus domestica, Petunia hybrida, Pisum sativum, Hordeum vulgare, Hyacinthus orientalis, Oryza sativa, Zea mays, and Picea abies that were registered in the NCBI database in November 2003 as well as Chlamydomonas reinhardtii AV622151. I indicates group I, II indicates group II. The chromosome map positions of each A. thaliana gene are indicated with numbers.

Fig. 4. Putative miR172 target sites in mRNAs of AP2 homologs. The underlined nucleotides are not complementary to miR172.

Fig. 5. Alignment of amino acid sequences of AP2 subfamily genes and RAV genes used in this study. Dashes indicate gaps. Asterisks above the alignment indicate the 60 amino acids used in the phylogenetic analysis. The ten specific amino acid residues in the AP2 repeat-1 domain of the ANT homologs are outlined.