Inferred contributions to the transcriptome by A- and D-genomes in a natural Gossypium allotetraploid and a synthetic diploid hybrid. (A) A- and D-genome contribution to the transcriptome for 1,383 homoeologous/allelic gene pairs. Each gene pair categorized based on a linear model analysis of three replicate measures of genomic contribution. 'Shared genes' are those with expression patterns that are conserved between allotetraploid G. hirsutum (AD1) and the diploid F1 hybrid (F1). (B) Diagrammatic representation of the conservation of genes with biased expression. (C) Scatterplot comparing the homoeolog expression log ratios found in the natural allotetraploid AD1 to the synthetic F1 hybrid. Each point represents a single gene. The correlation (r) and best-fit line are indicated in red. This correlation has a p-value less than 2.2 × 10-16, indicating that it is significantly different from zero. (D) Kernel density estimates of the homoeolog expression log ratios for all 1,383 genes from the 1:1 mix (green line), F1 hybrid (black line), and AD1 allotetraploid (red line) cotton. This plot demonstrates an erosion of equal contribution from both genomes and a shift toward more extreme values in the allopolyploid when compared with the F1 or 1:1 mix.