Fig. 1.—

Significance levels for comparisons of gene features. DE, de novo genes (782 genes); CO, common genes (26,474 genes); IN, intergenic ORFs (24,018 ORFs); TL, de novo genes with translational evidence (145 genes); TC, de novo genes with only transcriptional evidence (239 genes); TN, de novo genes without expression evidence (398 genes); TL⁺, TL genes with detected Poly(A) tails (65 genes); TL⁻, TL genes without detected Poly(A) tails (80 genes). π_n (π_s), polymorphism level in nonsynonymous (or synonymous) sites. CG, CHG, and CHH indicate DNA methylation in different contexts (H indicates A, C or T). Active histone modifications are histone markers H3K4me3, H3K36me3, and H3K9Ac in Data 24 of supplementary table S3, Supplementary Material online, and repressive histone modification is marker H3K27me3. P values were transformed into FDR values in the multiple comparisons. Five gene features with significant differences among the three types of de novo genes (TL, TC, and TN) are marked red. Detailed comparisons are shown in supplementary table S5, Supplementary Material online.