Fig. 3: Expression analysis for S. robusta multi-copy gene families.

a Expression divergence trend for multi-copy S. robusta families (n = 4444 families). The y axis denotes the percentage of nodes showing expression divergence in the phylogenetic tree of the family, while the x axis represents the number of S. robusta gene copies in the family. Average expression divergence percentages are indicated by red dots. Median expression divergence values significantly higher than the median of all nodes are highlighted with a star (P-value < 0.05, Wilcoxon rank-sum test, two-sided). b Heatmap showing pleiotropic families significantly enriched in upregulated genes for more than seven different conditions. The x axis represents the different conditions/experiments, whereas the y axis reports the families. The significance of the upregulation in a certain condition for a family is shown in –log₁₀(q-value) scale highlighted by a color gradient from gray to dark purple. Expansion and tandem enrichment of each family are highlighted in different colors on the right side of the heatmap. c Barplot showing family counts with significant condition-specific expression. The x axis represents the different conditions/experiments, whereas the y axis represents the number of families having significant expression bias for that condition. The color of the bars denotes the family age distribution. d Network showing families with significant specific expression in the three reproduction stages available. Families are represented with circles, while conditions are represented with diamonds. The color of the circles denotes the family age following the same color code as panel c. The edge’s width denotes the fraction of genes in the family that shows upregulation for the given condition, while the edge’s color represents the significance of the enrichment, following the same color code as panel b from gray to dark purple. Expansion and tandem enrichment of each family are indicated by the squares next to the gene family circles, also following the same color code as panel b. Source data are provided as a Source Data file. Numbers in superscript refer to families annotated in this Source Data file.