Supplemental Data

Files in this Data Supplement:

• Supplemental Figure 1 - Percent identity plot (PIP) of At5_3Mb vs all the collinear sequences in four Brassica BACs, 80A08, 4D11, 52O08, and 117M18. Three blacks boxes in the plot indicate sequence related transposons.
• Supplemental Figure 2 - Ks estimates between tandem duplicated genes. Green dotted lines classify orthologous genes in Arabidopsis (left) and B. rapa (right). Red dotted lines indicate the R3 duplication in the Arabidopsis-Brassica clade. Paralogous genes are represented as red and blue arrows in Arabidopsis (left) and B. rapa (right). Gene names and Ks values are given below and above the arrows, respectively. Deleted genes are denoted as blanks for each BAC listed on the right side. (A) A tandem array of two At5g10220 paralogs is present in At5_3Mb and its orthologous block 80A08 but not in its paralogous blocks, At5_25Mb and 80C09. (B) A tandem array of four At5g10140 paralogs is present in At5_25Mb and its orthologous block 80C09 but not in its paralogous block At5_3Mb or its four counterparts of Brassica. These two arrays may have been generated between R3 duplication and Arabidopsis-Brassica split. (C) A tandem array of two At5g10390 paralogs is present in At5_3Mb and its paralogous block At5_25Mb but not in their counterparts in Brassica. (D) A tandem array of two At5g10420 paralogs is detected in all Brassica BACs but not in their counterparts in Arabidopsis. These two arrays may have been generated before R3 duplication. All the Ks values are listed in Supplemental Table 3.
• Supplemental Table 1 - Pair wise alignment of homologous genes in seven duplication blocks
• Supplemental Table 2 - Pair wise comparisons of Ks values between homologous genes
• Supplemental Table 3 - Pair wise comparisons of Ks values from tandemly duplicated homologous genes