The Z Chromosome of the rattlesnake and the evolution of snake dosage compensation. (A) Normalized (log2) female/male genomic read coverage, female π, and windowed (30-gene) log2 normalized female/male gene expression. Known Z-linked markers (Matsubara et al. 2006) shown as blue blocks. In expression plot, red marks represent predicted estrogen response elements (EREs). On each plot, the pseudoautosomal region (PAR) and Recent Stratum are highlighted in gray and orange, respectively. (B) Normalized (log2) female/male kidney gene expression per gene (black dots) across the Z shown next to expression on Chromosome 5, a similarly sized autosome (left panels). The red dashed lines are the median ratios, and relative density is shown to the right of each panel. Gene expression (log2 RPKM) distributions for male and female across macrochromosomes, Z Chromosome, the PAR, and microchromosomes (center and right panels). Asterisks depict significant differences between autosomal and Z Chromosome expression. (C) Density plots of current and inferred ancestral patterns of gene expression (log2 RPKM) in male and female kidney, respectively. Dashed lines represent the median of each distribution. (D) EREs drive partial dosage compensation. The correlation (red line) between predicted EREs and female/male gene expression ratios in 100-kb windows (top panel) is shown with evidence for accumulation of EREs on the rattlesnake Z (bottom panel). Each bar shows the density of EREs found in specific chromosomes (rattlesnake Z and Anolis 6 shown in green) and genome-wide (gray bars). The asterisk depicts a significantly greater density of EREs on the rattlesnake Z than Anolis Chromosome 6.
