Fig. 2.

Expression data analysis to investigate dosage compensation in Acyrthosiphon pisum. a–d Comparison of the X-linked and autosomal genes transcription in males and both asexual and sexual females using increasing minimum TPM threshold to filter expressed genes. a The X/AA and XX/AA expression ratio of males (blue) and both asexual (red) and sexual (black) females, respectively. The dashed lines represent the dosage compensation criteria (X/A ratio between 0.95 and 1.05). b −Log20 (p value) of the Wilcoxon rank sum test comparing the expression of X-linked and autosomal genes. The dashed line represents p value = 0.05; all values below that line correspond to not significant Wilcoxon rank sum test. c, d Number of analyzed genes of A and B considering the expression filtration. Filters corresponding to dosage compensation for males are highlighted in gray, i.e., Wilcoxon rank sum test p value >0.05 and X/A ratio between 0.95 and 1.05. e–l Distribution of expression of autosomal and X-linked genes. Expression is represented for all (e, i), female-biased (f, j), male-biased (g, k) and unbiased (h, l) genes for males (blue) and females (red). These classes of expression have been determined using EdgeR (see “Methods”). The violin plots represent the gene density at each log2(RPKM + 1) level. Dashed lines correspond to the median of expression of autosomal gene in each category. m, n Number of genes belonging to each gene class on the X chromosome and on the autosomes