Transgene insertion locations and expression

For each transgene insertion, we provide the following information (column descriptions): 1) Promoter, Chromosome, Cytogenetic location, Sequence coordinate (Drosophila Genome release 5), Affected gene, Proximal gene (within 10 kb), distal gene (within 10 kb), Whether the transgene is in or near a testis-enriched gene, Whether the transgene is in or near a testis-biased gene, mean beta-galactosidase activity, standard deviation of beta-galactosidase activity, mean relative expression measured by qRT-PCR, standard deviation of relative expression measured by qRT-PCR. Additional notes are provided at the bottom. Format is .xls

Identification of the pseudo-autosomal region (PAR) on the Z chromosome of the European crow.

(A) F:m DNA sequencing coverage along the Z chromosome. (B) heterozygosity levels across the Z chromosome in females (light blue) and males (gray). A drop in both measures after 688 kb defines the end of the PAR. (C) One Mb of Z chromosome alignment between the flycatcher and the European crow. Lines between the Z represent orthologous regions found between the two species. Red: protein coding genes. Blue: non-coding regions. The vertical red dashed line marks the end of the PAR region in the European crow in all panels.</p

Boxplot showing the distribution of the number of associated peaks per expressed gene in the autosomes and the Z chromosome in a region of 20 kb upstream and downstream of the focal gene.

Boxplot showing the distribution of the number of associated peaks per expressed gene in the autosomes and the Z chromosome in a region of 20 kb upstream and downstream of the focal gene.</p

Number of mapped reads after filtering steps described in the methods section.

The libaries were down-sampled to the library with the lowest number of reads. The normalization factor indicates whichi proportion of original reads was kept. Data is shown seperately for liver and spleen. (XLSX)</p

Autocorrelation of gene expression present on the Z chromosome.

Red vertical line shows the PAR border. Blue lines represent autocorrelation values significantly different from zero. Except for the PAR region, there is no clear trend of clusters that would point at local centers of dosage compensation. Liver: upper panel. Spleen: lower panel. (TIFF)</p

Relationship between epigenetic features, gene expression and dosage balance on the Z chromosome (DB).

(A,D) Linear regression of log2(f:m) peak height to gene expression. Peak height is measured as read counts in peaks. Boxplots depicting (B,E) log2(f:m) ratios of peak height in regulatory regions of dosage balance (DB) and not DB genes. (C,F) log2(f:m) ratios of 5mC methylation in CpG islands of DB and not DB genes. Boxes in boxplots encompass interquartile ranges across genes, whiskers extend to 1.5 x the interquartile range. Wilcoxon-test statistical significance levels: 0.0001 ‘***’, 0.001 ‘**’, 0.01 ‘*’. Data show for liver (A, B, C) and spleen (D, E, F).</p

Sex-specific CpG methylation divergence genome-wide.

Differentially methylated features (genes or CpG islands) were identified with a beta-binomial regression using methylation counts implemented with a general experimental design framework in DSS. FDR-corrected -log10(p-values) for sex divergence are plotted along the bottom first and third panels for liver and spleen, respectively, with the dashed line indicating FDR-corrected significance (0.05). Bootstrap sampling log2(F/M) values are shown along bottom second and fourth panels. (TIFF)</p

Correlations between sex-specific DNA methylation divergence.

(log2(F/M)) and expression (log2(F/M)) across both tissues for both CpG islands and directly over gene bodies for Z-linked transcripts. CpG island expression level was determined as the expression level of the closest genomic transcript. Spearman’s rho is written for each facet, and for each dosage compensation state (dosage balanced, or unbalanced, as identified from expression data). (TIFF)</p

Boxplot of female to male read coverage distribution from whole genome shotgun sequencing of one individual of each sex as calculated in 50 kb windows, in chromosome 1 (chr1), chromosome 2 (chr2), the pseudoautosomal region (PAR) and the Z chromosome without the PAR.

F/M coverage ratio on the shown autosomes and the PAR lie near a ratio of 1 (red line), whereas the hemizygous part of the Z lies close to a ratio of 0.5 (grey line). (TIFF)</p

Boxplots presenting log₂ gene-centred peak height distribution broken down into four quantiles (Q1 –Q4).

A: autosomes, Z: Z chromosome. Upper panel liver, bottom panel spleen. (TIFF)</p