Fig. 4.

Subgenomic expression divergence during embryogenesis in allotetraploid common carp. (a) Expression levels of the two subgenomes. The boxplot was based on homoeologous gene pairs with a summed expression of > 1 TPM in at least one developmental stage. The expression levels of genes in subgenomes A and B and the sum of both copies are included. (b) Percentage of dominant and balanced expression of genes during embryogenesis. Dominant expression is defined as an expression divergence larger than 2-fold. (c) The expression levels of dominant and balanced expressed homoeologous genes. The expression levels of the balanced genes were higher than those of the suppressed genes, but lower than those of the dominant genes. (d) Expression patterns for HGs switching their dominant patterns during development. In total, 275 HGs showed a dominant switch from A to B, and 202 from B to A. The turning point occurred at the S4 (neurula) stage. One asterisk indicates a p value < 0.05, two asterisks indicate a p value < 0.01, and three asterisks indicate a p value < 0.001. The significance for a and c was tested with a two-sided Wilcoxon rank-sum test.