Figure 2—figure supplement 1.

(A) Proportion of genes activated only from one homeolog or from both homeologs at stage 8, as compared to their homeolog activation patterns at stage 9. (B) Biplots showing L dominant (red) or S dominant (blue) activation at stage 8 (left), that resolves to more balanced homeolog activation patterns at stage 9. Each gene is the same color in both plots. (C) Biplot comparing log2 fold all stage 9 activation over triptolide treated embryos for the S homeolog (x axis) versus the L homeolog. (D) Proportion of genes activated symmetrically or asymmetrically from the L or S subgenomes, stratified into whether there is a maternal contribution for either homeolog (MZ) or not (Z), for primary activated genes, all stage 9 activated genes, and stage 10.5 activated genes. p Values are from χ-squared tests, 4 d.o.f. (E) Proportion of genes activated symmetrically or asymmetrically from the L or S subgenomes from stages 10–13 in differentiated lineages. Top plots represent all genes increased at each stage, bottom plots represent genes with maternal contribution <1 TPM. Lineage-specific gene expression data are from Johnson et al., 2022. (F) Proportion of genes encoded on both subgenomes that change homeolog activation patterns in a differentiated lineage in stages 10–13. (G) Concordance of homeolog activation patterns across the differentiated lineages at stages 10–13, for all genes up in at least two different lineages (top) or only genes with maternal contribution <1 TPM (bottom). (H) Boxplots showing log2 L versus S expression ratio for each differentiated lineage over stages 10–13, in the whole transcriptome. N = 8271 homeolog pairs. (I) Zoom of boxplots in (H), demonstrating a gradual bias toward L-dominant expression over time. (J) Significantly (FDR <0.05, Fisher’s exact test, two-sided) enriched Gene Ontology terms in genes activated from both homeologs, as compared to genes activated from only one subgenome. (K) Boxplots of non-synonymous to synonymous substitution rate ratio (dN/dS) shown on a log10 scale, for genes activated from both subgenomes or only one subgenome (p=0.15, Kruskal-Wallis test; median L=0.15, LS = 0.14, S=0.14). All gene groups trend toward stabilizing selection. N = 465, 585, 305 for L, L+S, and S groups, respectively. (L) Boxplots of CDS percent similarity for activation groups as in (K) (p=0.23, Kruskal-Wallis test). For all boxplots: center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers.