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.

补充文件2：表S1。各样本的原始读段、修剪后读段、唯一比对读段数量及比对率。
表S2：Ovd基因靶标的表达量（分别对应DESeq2的标准化计数与edgeR的每百万转录本片段计数（Counts Per Million, CPM）），以及各相对于亲本物种的成对比较经错误发现率（False Discovery Rate, FDR）校正后的p值。基因表达失调的分类依据所用两种差异表达分析工具的一致性结果判定。在不育条件下出现表达失调，且在F28可育样本与亲本样本间呈加性表达或无差异表达的基因，将被标记为潜在不育靶标。
表S3：Ovd靶标的染色体分布情况，其中不育靶标的基因ID以粗体标注。基因簇的基因符号以黄色高亮显示，并附带簇内基因间的距离信息。先前已定位的常染色体数量性状位点（Quantitative Trait Locus, QTL）内的基因位置以灰色高亮标注。
表S4：BLASTp比对结果，展示各簇内基因的黑腹果蝇（Drosophila melanogaster）同源基因预测结果。随机匹配概率低于0.01的黑腹果蝇基因以粗体标注。
表S5：Ovd已定位靶标的潜在顺式调控变异信息。“Adf-1位点”指在转录起始位点（Transcription Start Site, TSS）上游3000 bp范围内预测到的结合位点总数。“Total_pol”指Adf-1位点处检测到的多态性总数。“Fixed”指在鉴定出的Adf-1位点上，拟暗果蝇拟暗亚种（Drosophila pseudoobscura pseudoobscura, D. p. pseudoobscura）与拟暗果蝇波哥大亚种（Drosophila pseudoobscura bogotana, D. p. bogotana）之间存在的固定核苷酸差异。其中有一个基因的多态性组合可实现两个亚种的区分。“ASE”为等位基因特异性表达（Allele Specific Expression, ASE）分析结果，“Mode”用于区分存在各类顺式调控现象的基因与其他基因。固定替换数指在−500至+200（记为500）、−1000至+200（记为1000）、−2000至+200（记为2000）以及−3000至+200（记为3000）的基因区域内，两个亚种间存在的固定核苷酸差异总数。