1. Supplementary figure S3. Diagram showing the effects of removing data from particular organ types on the relative percentage of gene pairs showing reciprocal expression. Removal of data from siliques showed the largest effect (ca. 20%; x 2, P= 0.0363).

2. WGDsTandems A B * ** * * * * * Relative %: 0102030 Color key Supplementary figure S4. Expression gains and losses by different organ type, developmental stage, and cell type. Summary of Fisher’s exact tests between expression gain and expression loss from MRCA analysis in each condition (i.e., organ type, developmental stage, or cell type). A statistically significant difference after 5% false discovery rate correction is labeled with a star (*: Q < 0.05; **: Q < 0.01). (a) A comparison of the relative percentage between expression gain and expression loss in 63 different developmental stages and organ types in both WG duplicates and tandem duplicates. The 63 different developmental stages and organ types are listed in supplementary table S5. (b) A comparison of the relative percentage between expression gain and expression loss in 20 different developmental stages and cell types in roots. The 20 different developmental stages and cell types of roots are listed in supplementary table S6.

3. A) WGDs B) Tandems Supplementary figure S5. Box plots showing a comparison of the synonymous substitution rate (Ks) between gene duplicates with asymmetric sequence evolution and those without asymmetric sequence evolution (i.e., symmetric sequence evolution). (a) WG duplicates (t-test: P = 0.7103; Wilcoxon signed-rank test: P = 0.7204). (b) Tandem duplicates (t-test: P = 0.4043; Wilcoxon signed-rank test: P = 0.2329).

4. Supplementary figure S6. Boxplots showing a comparison of the synonymous substitution rate (Ks) between the WG duplicates and the tandem duplicates (t-test: P = 1.659e-05; Wilcoxon signed-rank test: P = 3.221e-13).

5. Supplementary figure S7. Amino acid alignment of a pair of duplicated genes, BSU1 and BSL1, and their orthologs from three outgroup species, Carica papaya, Populus trichocarpa, and Vitis vinifera. Red dots indicate the positively selected sites of BSU1 that were detected based on the branch-site test of positive selection using the program Codeml in PAML. The blue box indicates the Kelch-repeat domain and the red box indicates the phosphatase domain.