Supplemental Data

Files in this Data Supplement:

• Supplemental Table 1
• Supplemental Table 2
• Supplemental Table 3
• Supplemental Table 4
• Supplemental Figure 7 - Sequence alignments of AtbHLH domains from apparently duplicated regions of the At-genome. The groups of AtbHLH proteins in this figure potentially derived from duplication events were deduced from the locations of closely related AtbHLH proteins (as determined from the closeness of the entry numbers in the alignment shown in Figure 1) in apparently duplicated regions in the genome as shown in Figure 4. Each protein is designated by the entry number and PID number used in this study. The AtbHLH number and the chromosome where each protein is located are also indicated. Three types of putative duplication and the corresponding proteins involved are summarized in this table: (A) tandem arrays, (B) intra-chromosomal duplications, and (C) inter-chromosomal duplications. In the alignments, the percentage of amino acid conservation is illustrated by shading. Dark blue indicates identical residues and light blue indicates similar residues. Dots denote gaps. Shading was done using the Mac box shade program with 50% conservation shading.
• Supplemental Figure 1-1 - Fit of the AtbHLH proteins to the predictive consensus motif. Multiple sequence alignment of the bHLH domain of the AtbHLH proteins identified in this study. The alignment maintains the order shown in Figure 1. The proteins are named according to their entry number (EN) and protein identification numbers (PID numbers). The numbering of the position within the bHLH motif as defined here and the designation of the basic, helix, and loop regions are indicated at the top of the figure. The positions on which the consensus motif described in Table 1 are based are highlighted in gray. The amino acids that constitute the consensus motif and their position are indicated at the bottom of the figure. The total number of mismatches from the consensus motif is indicated in the left-hand column and the mismatches in the basic region are indicated in the right-hand column.
• Supplemental Figure 1-2
• Supplemental Figure 2 - Sequence alignments of clusters of AtbHLH proteins with high homology within their bHLH domains. These sequence alignments are subsets of those shown in the complete alignment of the 147 bHLH proteins reported in this study (Figure 1). The proteins included here have an amino acid sequence identity higher than 50% in their bHLH domains. For each subset of proteins, within the cluster (see Figure 1 and Table 2 for entry number and accession number), the percentage of amino acid conservation is illustrated by shading. Black boxes indicate identical residues with 100% conservation, red boxes indicate conserved residues (≥50%), and yellow indicates similar residues. Dots denote gaps. Shading was done using the Mac box shade program with 50% conservation shading. The percentage of identical amino acids within each subgroup of bHLH domains is indicated on the right. Asterisks indicate the amino acids that are not identical within each subgroup shown.
• Supplemental Figure 3 - Neighbor joining (NJ) phylogenetic tree of the bHLH domains of the AtbHLH proteins with branch length values. NJ unrooted phylogenetic tree (cladogram) constructed with PAUP 4.0. The proteins are named according to their protein identification numbers (see Figure 1 and Table 2). The tree was constructed using the amino acid sequence of the bHLH domain for each protein. The alignment on which the tree was constructed is shown in Figure 1.
• Supplemental Figure 4 - Bootstrap NJ phylogenetic tree of the At-bHLH-protein bHLH domains. The tree was constructed using PAUP 4.0 and 1000 replicates. The distance parameters selected are the total character difference among site rate variation and randomly initiated seed. The proteins are named according to their protein identification number (see Figure 1 and Table 2). The tree was constructed using the amino acid sequence of the bHLH domain for each protein and the alignment on which the tree is based is the one shown in Figure 1.
• Supplemental Figure 5-1 - Sequence alignment of AtbHLH domains indicating the phylogenetic clade to which they belong and the intron distribution pattern. The sequence alignment is as shown in Figure 1, and for each protein the phylogenetic subfamily is indicated in the left-hand column. The subfamilies are those defined in the phylogenetic tree shown in Figure 2. An N indicates that the protein does not form part of any of the defined subfamilies. The right-hand column indicates the intron distribution pattern within the bHLH domain as defined in Figure 3. The amino acids that constitute the consensus motif and their positions are indicated in the rectangle at the bottom of the figure.
• Supplemental Figure 5-2
• Supplemental Figure 6 - Maximum parsimony majority rule 50% consensus phylogenetic tree of the At-bHLH-protein bHLH domains. The 50% consensus tree was constructed from a full heuristic search of 1000 trees using PAUP 4.0. The parameters selected were total character difference among site rate variation and randomly initiated seed. The proteins are named according to their protein identification number (see Figure 1 and Table 2). The tree was constructed using the amino acid sequence of the bHLH domain for each protein and the alignment on which the tree is based is the one shown in Figure 1. The other parameters used were random seed initiation, stepwise addition, and collapsing of zero length branches. Parsimony noninformative characters were excluded from the analysis. Gaps were treated as missing data. The tree is unrooted and topological constraints were not enforced.