Fig. 1

Dosage compensated and non-compensated genes in male and female fibroblast cells in birds. A Amniote phylogeny and sex determination. B Numbers of active TSS (transcription start sites) and genes in avian fibroblast cells. C Numbers of differentially expressed genes between male and female fibroblast cells in chicken. D MDS (multi-dimensional scaling) plot for chicken fibroblast samples. Two groups of samples are clearly separated by dimension 1. CAGE-seq samples labeled by “C07-12,” RNA-seq samples by “male” and “female”. E Hierarchical clustering of sex chromosome gene expression determines fibroblast sex identity in chicken. Male samples lack chrW gene expression (arrow). F Expression profiles of known sex markers in chicken (C11 and C12: male; C7-10: females). FDR values are shown. G Expression fold changes (FC) of genes located on chicken sex chromosomes and autosomes. Male boxplot for genes with log2FC > 0, female log2FC < 0 (FDR < 0.05). Genes localized on chrW demonstrated the greatest differences, while chrZ genes have relatively narrow FC ranges between male and female. Wilcoxon test was used for statistical estimates. H Numbers of differentially expressed (DE) genes between male and female by chicken chromosomes. Arrows indicate sex chromosomes. I Percentage of compensated genes (FDR > 0.05) on chrZ in birds. On average 78% of genes show no DE between sexes in fibroblast cells (with no FC cutoff, excluding emu and peacock). For emu, compensation ratio is 29% when PAR is excluded, blue bars indicate percentage of non-DE genes on entire chrZ. Peacock excluded due to absence of chrZ in its genome assembly