Table 2.
Genome-wide subgenome expression bias.
| A-biased | B-biased | A completely dominant | B completely dominant | Balanced | |
|---|---|---|---|---|---|
| Constitutive | 13 (0.15%) | 14 (0.16%) | 0 | 0 | 8789 (99.7%) |
| Seedling leaf | 352 (4.4%) | 335 (4.2%) | 0 | 0 | 7234 (91.3%) |
| Mainstem leaf | 155 (1.9%) | 153 (1.9%) | 31 (0.38%) | 30 (0.37%) | 7962 (96.3%) |
| Lateral leaf | 361 (4.4%) | 341 (4.2%) | 49 (0.6%) | 51 (0.62%) | 6964 (94.2%) |
| Vegetative shoot tip | 660 (7.9%) | 606 (7.3%) | 38 (0.46%) | 39 (0.47%) | 7473 (83.8%) |
| Root | 742 (8.7%) | 745 (8.7%) | 43 (0.5%) | 45 (0.53%) | 6990 (81.6%) |
| Nodules | 574 (6.8%) | 516 (6.1%) | 50 (0.59%) | 50 (0.59%) | 7288 (86%) |
| Reproductive shoot tip | 781 (9.1%) | 790 (9.2%) | 43 (0.49%) | 38 (0.43%) | 6913 (80.7%) |
| Perianth | 922 (11%) | 934 (11.19%) | 41 (0.49%) | 49 (0.59%) | 6412 (76.8%) |
| Gynoecium | 110 (1.2%) | 130 (1.5%) | 20 (0.23%) | 20 (0.23%) | 8349 (96.8%) |
| Androecium | 59 (0.71%) | 58 (0.7%) | 16 (0.19%) | 21 (0.25%) | 8161 (98.1%) |
| Aerial gynophore tip | 184 (2.2%) | 219 (2.6%) | 27 (0.32%) | 30 (0.35%) | 8064 (94.6%) |
| Subterranean gynophore tip | 585 (7%) | 587 (7.1%) | 42 (0.5%) | 34 (0.41%) | 7076 (85%) |
| Pattee 1 pod | 87 (1%) | 66 (0.79%) | 20 (0.23%) | 24 (0.29%) | 8193 (96.7%) |
| Pattee 1 stalk | 129 (1.6%) | 107 (1.3%) | 29 (0.35%) | 33 (0.4%) | 8023 (96.4%) |
| Pattee 3 pod | 431 (5%) | 409 (4.8%) | 31 (0.36%) | 36 (0.42%) | 7633 (89.4%) |
| Pattee 5 pericarp | 257 (3%) | 231 (2.7%) | 26 (0.31%) | 30 (0.35%) | 7966 (93.6%) |
| Pattee 5 seed | 506 (5.74%) | 492 (5.58%) | 42 (0.48%) | 40 (0.45%) | 7736 (87.75%) |
| Pattee 6 pericarp | 254 (3%) | 246 (2.9%) | 19 (0.23%) | 33 (0.39%) | 7876 (93.5%) |
| Pattee 6 seed | 343 (4%) | 342 (4%) | 32 (0.38%) | 34 (0.4%) | 7757 (91.2%) |
| Pattee 7 seed | 273 (3.3%) | 241 (2.9%) | 36 (0.43%) | 24 (0.29%) | 7811 (93.2%) |
| Pattee 8 seed | 308 (3.8%) | 290 (3.6%) | 39 (0.48%) | 28 (0.34%) | 7478 (91.8%) |
| Pattee 10 seed | 281 (3.6%) | 267 (3.4%) | 56 (0.71%) | 32 (0.41%) | 7239 (91.9%) |
For each tissue expression bias between the set of 8816 putative homeologous pairs was calculated using DESeq2. Constitutive refers to the A or B copy and is significantly higher expressed in all tissues sampled. A biased are A pairs significantly higher expressed in A and B biased are B pairs significantly higher expressed in B. Completely A or B dominant are pairs that are expressed in A or B while the other is not expressed. Balanced is no expression difference between the A or B copy. Percentages in parentheses indicate percentage of the total pairs expressed in that tissue type.