Additional file 2 of Divergence of X-linked trans regulatory proteins and the misexpression of gene targets in sterile Drosophila pseudoobscura hybrids

Additional file 2: Table S1. Number of raw, trimmed, and uniquely mapped reads along with the mapping rate for each sample. Table S2. Expression of Ovd gene targets (in normalised counts and CPM for DESeq2 and edgeR respectively) and the FDR-corrected p-values for each pairwise comparison relative to parental species. Classification of misregulation is determined by the consensus result of both differential expression tools used. Genes misregulated in both sterile conditions and with additive or non-differential expression between the F28 fertile and parentals are highlighted as putative sterility-targets. Table S3. Chromosome distribution of Ovd targets with sterility targets Gene IDs bolded. The gene symbol of gene clusters are highlighted in yellow along with the distance between genes in the cluster. The location of genes within previously mapped autosomal QTLs is highlighted in grey. Table S4. BLASTp results showing putative D. melanogaster orthologs of genes within clusters. D. melanogaster genes with probability of random match lower than 0.01 are bolded. Table S5. Potential cis changes among mapped targets of Ovd. ‘Adf-1 sites’ is the total number of putatitive binding sites found 3000 bp upstream of the TSS. ‘Total_pol’ is the total number of polymorphism found at Adf-1 sites. ‘Fixed’ refers to fixed nucleotide changes between D. p. pseudoobscura and D. p. bogotana at identified Adf-1 sites. For one gene the combination of polymorphisms allows differentiation between the subspecies. ‘ASE’ is the result of allele specific expression and ‘Mode’ differentiate genes that show some form of cis-regulation form others. Fixed substitutions is the total number of fixed nucleotide changes between subspecies in the −500 to +200 (500), −1000 to +200 (1000), −2000 to +200 (2000) and − 3000 to +200 (3000) gene regions.