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). Slide 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 Fishers
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. Slide 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). Slide 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). Slide 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.