Partitioning of expression patterns in allopolyploid Gossypium , A- and D-genome contrast. Graphs inset into panels I to XII represent the possible expression patterns between two diploids and an allopolyploid derivative, where statistically differential expression is indicated by different vertical levels in each graph. Thus, for example, panel I in shows genes for which the paternal parent was differentially expressed and up-regulated relative to the allopolyploid, and the latter was up-regulated relative to the maternal parent. The total number of genes falling into each category is shown (N), as are the density distributions of expression levels (y-axis) for the genes involved in that particular expression pattern (maternal = dark blue; paternal = green; allopolyploid = light blue). In each of panels I to XII the x-axis represents standardized expression intensity. The average for the entire experiment is shown in each panel as the black horizontal line. All categories of gene expression are observed in both allopolyploids, although in remarkably different ratios (See Figure 5). Expression dominance of the paternal, G. thurberi genome in 2(A2D1) is shown by panels II and XI in Figure 4 (contrast with IV and IX), whereas the same phenomenon is shown (albeit to a lesser extent) for the G. arboreum genome in 2(A2G1) (same panels and contrast, Figure 5). In both cases, expression dominance reflects approximately equal amounts of up- and down-regulation to mimic the expression phenotype of the dominant parent. Transgressive up-regulation in each allopolyploid is partitioned into the possible constitutive categories and is shown by panels V, VI, and VIII; similarly, down-regulation is shown by panels III, VII, and X. The middle panel in each figure shows the distribution of expression divergence of each parent relative to the polyploid, with the maternal contrast on the y axis and the paternal contrast on the x axis, with colors corresponding to those used in the insets in panels I to XII.