Extended Data Fig. 5: Transcriptome and translatome comparison across different tissues and genotypes.

a, Log₂-fold changes (Log₂FC) between Z^KOZ^KO and ZZ genotypes for both autosomal (Non-targets: n = 7279 (RIBO), n = 7566 (RNA); Targets: n = 2238 (RIBO), n = 2309 (RNA)) and Z-linked protein-coding genes (Non-targets: n = 197 (RIBO), n = 220 (RNA); Targets: n = 264 (RIBO), n = 292 (RNA)). Two-sided Wilcoxon test P-values between data types or target groups are indicated above and below. Log₂FC estimates are either based on transcriptome (RNA) or translatome data (RIBO, indicated by dashed lines) of E3 embryo heads. Genes with FPKM > 1 were used and values were normalized using either the median of autosomal non-target transcriptome or translatome expression. b, Median and interquartile ranges of ratios of current versus proto-Z (ancestral) translation for Z-linked non-targets (n = 174) and Exp-Z (n = 188) genes for males and females (log₂). Reference lines indicate ratios of − 1 (half ancestral expression), 0 (equal expression), and 1 (twofold ancestral expression). Statistical significance is indicated above as TOST (Two One-Sided Tests) Wilcoxon equivalence test (green indicates significance within equivalence bounds (reference value ± 0.5, Methods), gray indicates non-significance) and two-sided one-sample Wilcoxon test (red equals significant deviation from reference value, gray equals non-significant deviation). c, Female-to-male expression level ratios (log₂) for Exp-Z and Other-Z genes in adult brain (Exp-Z: n = 203 (RIBO), n = 215 (RNA); Other-Z: n = 270 (RIBO), n = 297 (RNA)) and embryonic head (Exp-Z: n = 201 (RIBO), n = 212 (RNA); Other-Z: n = 257 (RIBO), n = 282 (RNA)). Two-sided Wilcoxon test P-values between data types or between target groups are indicated above and below. Ratios were calculated using either transcriptome (RNA) or translatome data (RIBO, indicated by dashed lines). Genes with FPKM > 1 were used and values were normalized using either the median of autosomal transcriptome or translatome expression. Statistical significance was assessed as in b). d, Female to male translational efficiency (TE) ratios (log₂) for Exp-Z, Other-Z and Autosomal genes in adult brain (Exp-Z: n = 194; Other-Z: n = 259; Autosomal: n = 9843) and embryonic head (Exp-Z: n = 199; Other-Z: n = 246; Autosomal: n = 9276). Two-sided Wilcoxon test P-values between target groups are indicated above. Genes with FPKM > 1 were used and values were normalized using the median of autosomal TE ratios. All box plots show the median, 25th–75th percentiles, and whiskers extending to 1.5× the IQR.