Supplemental Data

Files in this Data Supplement:

• Supplemental Figure 1 - Summary table of MEME analyses for CNL and TNL proteins. Motifs from the MEME analyses in the supplemental files were consolidated and manually aligned in a spreadsheet to allow the comparisons of motif composition and configuration. Because motif analyses were performed for each domain separately for each of the CNL and TNL families of proteins, numbers and colors are specific only to that domain. The MEME “score” for the overall match of the protein to the motif models is given as a P value. Missing motifs may indicate either a deleted domain or a poor match (>e-04).
• Supplemental Figure 2 - Diagonal plot of a comparison of the Arabidopsis Col-0 genome against itself using BLAST. All pairs of genes with expectation of <1e-20 and inferred amino acid identity of at least 40% with an overlap of greater than 100 amino acids are shown as individual elements. Segmental duplications result in diagonal lines. Genes encoding NBS-LRR, cytochrome P450, and LRR-protein kinases are colored red, green, and blue, respectively. All other genes are colored shades of gray reflecting their similarity.
• Supplemental Figure 3 - Distribution of genes encoding CNL and TNL, cytochrome P450, and LRR-kinase proteins relative to segmental duplications in the Arabidopsis genome. The boundaries of all 81 segmental duplications containing at least 10 genes in common previously identified by Simillion et al. (2002) are joined by blue lines and are listed to the right. The different classes of CNL and TNL related genes are color coded, and those with greater than 60% identity are joined with red lines.
• Supplemental Table 1 - Cluster analysis of CNL and TNL genes in the Col-0 genome. To facilitate sorting, Arabidopsis gene identifiers were modified so that the first number indicates the chromosome and the numbers after the decimal are the gene number. The gene group and subgroup refer to categorization described in the text. The numbers identify clusters of genes that include at least one CNL and TNL or related gene within a maximum of eight adjacent open reading frames. The column labeled “cluster type” indicates the relationship of genes within the cluster; the four adjacent columns indicate how each cluster was designated in the summary table (Table 4).
• Supplemental Table 2 - Distribution of multigene families encoding CNL and TNL, cytochrome P450, and LRR- kinase proteins in segmental duplications in the Col-0 genome.