Fig. 4: Evolution of sex-biased genes during transitions to monoicy.

a, Comparison of gene expression levels within species pairs, in log₂(TPM + 1), using PSO gene sets. Mo, monoicous. The numbers of FBGs and MBGs among PSOs are displayed. Note that only the sex-biased genes with a single-copy ortholog in the corresponding monoicous species are displayed in the plots (in other words, the sex-biased genes represented in the plots are a subset of the sex-biased genes identified within each dioicous species). The boxes represent the interquartile ranges (25th and 75th percentiles) of the data, the lines inside the boxes represent the medians, and the whiskers represent the largest/smallest values within 1.5 times the interquartile range above and below the 75th and 25th percentiles, respectively. The statistical tests are permutation t-tests using 100,000 permutations. Paired two-sided t-tests were used for comparisons between sexes of the same species (dioicous species). b, Comparisons of similarity index values (Pearson coefficients) between expression profiles (in log₂(TPM + 1)) of PSOs between monoicous and dioicous species pairs. The figure represents male versus female similarity indexes in relation to the monoicous expression profiles. Note that similarity indexes are represented separately for sex-biased genes in females (red) and in males (blue), as well as for unbiased genes averaged across sexes in the dioicous species (black). Pearson coefficients were plotted for each species pair in increasing order of the proportion of sex-biased genes among expressed genes of dioicous species (x axis). The asterisks in the top panel represent significant differences between Pearson coefficients, taking into account the correlations between compared gene sets, using the cocor package in R. The red and blue asterisks indicate significant differences between the Pearson coefficients of female (red) or male sex-biased genes (blue) and those of unbiased genes. The black asterisks in the top panel indicate significant differences of Pearson coefficients of unbiased genes between males and females. Significant differences of coefficients between sex-biased genes in females and males are indicated directly on the plot. *0.01 < P < 0.05; **0.001 < P < 0.01; ***P < 0.001. See also Extended Data Fig. 4 and Extended Data Fig. 5. Unb., unbiased; SBG, sex-biased genes. c, Fraction of FBGs (red), MBGs (blue) and non-biased genes (grey) with an absolute value of ΔX > 1 and FC > 1.5, calculated within species pairs (on PSOs). The percentages are calculated on the total number of orthologs in each category. Downregulated genes in the monoicous species are represented below the y = 0 line (ΔX < −1); upregulated genes in the monoicous species are represented above the y = 0 line (ΔX > 1). The asterisks indicate a significant over-representation of FBGs or MBGs with an absolute ΔX > 1 compared with the proportion of unbiased genes with ΔX > 1, tested using Fisher exact tests. d, Sequence divergence, measured as dN/dS (ω), between dioicous and monoicous species calculated within species pairs (PSOs). The statistical tests are permutation two-sided t-tests using 100,000 permutations, and the P values are displayed in parentheses. *0.01 < P < 0.05; **0.001 < P < 0.01; ***P < 0.001. e, Principal component (PC) analysis plot of all the RNA-seq samples, using ASOs. Monoicous species are plotted in orange, female samples in red and male samples in blue.