Differential expression and genome-wide expression dominance in Gossypium allopolyploids. A. Synthetic allopolyploid 2(A2D1) generated from the diploid parents G. arboreum and G. thurberi. G. arboreum was the maternal parent in each cross. Bold text indicates the total number and fraction of genes diagnosed as differentially expressed in each contrast. Also shown for each contrast is the partitioning of the total number of differentially expressed genes into the direction of up-regulation; these numbers are indicated by the non-bold text. For example, in panel A, 13,863 genes are indicated as being differentially expressed between G. arboreum and the synthetic allopolyploid. Of these, 7792 were up-regulated in the synthetic allopolyploid, and 6071 were up-regulated in G. arboreum. Differential expression between each allopolyploid and its in silico mid-parent is shown in the middle of each triangle. Around 53.0% of the 40,430 unigenes were differentially expressed between diploids, with a range of 4.4% to 34.3% between diploids and their allopolyploid derivatives. Expression dominance is illustrated by the eight-fold asymmetries in differential expression between the allopolyploids and their diploid antecedents. B. Genes were ordered by their normalized, standardized expression intensity in the allopolyploid (black line). The expression intensity of the parents was superimposed (maternal = blue; paternal = green) to illustrate the expression level similarity between the dominant genome and the allopolyploid. Thus, variance around the green dots (the dominant genome) is lower than around the blue dots. Thus, expression dominance is bidirectional with respect to the status of the G. arboreum expression phenotypes in the two allopolyploids.