Fig. S1. A flowchart illustrating the main steps of our sequence processing, assembly, expression and variant call analysis.

Fig. S2. Length distribution of contigs with a significant pattern of gene expression.

Fig. S3. Hierarchical clustering of the gene expression data for the six males and six females investigated in this study for the A. autosomal and B. Z-linked genes. Clustering was carried out using Euclidean distance with complete linkage. The number at each node represents bootstrap support based on 1000 replicates. Values less than 50 are not shown.

Fig. S4. 2 Mb sliding average of the M/F ratios of expression in A. red jungle fowl and B. Kentish plover plotted against the median gene position along the chicken Z chromosome. The HMH locus is approximately at position 26 Mb.

Fig. S5. Count distribution of various types of nucleotide repeats throughout the autosomal contigs with putative avian origins.


Table S1. Examining the number of contigs that passed various filtering thresholds for different minimum number of reads per million mappable reads (PMMR) and minimum number of replicates (MNR) in either of sexes.

Table S2. Gene ontology categories enriched among female-biased transcripts.

Table S3. Gene ontology categories enriched among male-biased transcripts.

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