RNA-seq analysis of embryonic chicken blastoderms and embryonic day 4.5 (stage 26) gonads. (A) Differentially expressed annotated genes (Ensembl-based). Number of genes showing either male-biased differential expression (FDR <0.05; blue) or female-biased expression (FDR <0.05; red) in blastoderms and E4.5 gonads. (B) Chromosomal allocation of differentially expressed genes, based on annotated gene data. In blastoderms, female biased genes were located on the W or W_random chromosome (red), the autosomes (grey), or the un-assembled Un_random chromosomes (green). One Z-linked gene showed female-biased expression (aqua). The vast majority of male-biased genes were Z-linked (aqua), and autosomal (grey). Two were on Un_random chromosomes and zero on the W chromosome. A similar pattern was observed in the gonads, with the majority being Z-linked in males, and W-linked or on the Un_random in females. (C) Bar graph illustrating the number of genes with sexually dimorphic expression in at least one tissue on the W, Z, autosomal and Un_random chromosomes. Genes were tested for different patterns of sexually dimorphic expression between tissues, and are grouped as to whether they show a significantly larger female: male ratio difference in the blastoderms (purple), the gonads (yellow) or whether no significant difference is observed (aqua) (FDR <0.05) (See also Additional file 4, Table S1c). (D) Bar graph of genes of genes that are significantly sexually dimorphic in at least one tissue on the W, Z, autosomal and Un_random chromosomes, similar to Fig. 1C). Here, genes are grouped based on a change in average expression between tissues. Shown are the number of genes which are significantly more highly expressed in the blastoderms (purple), higher in the gonads (yellow), and no significant change (blue) (FDR <0.05) (See also Additional file 4, Table S1c).