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Additional file 1. FAIRE and Control libraries coverages. Number of reads and coverage of X chromosome (X) and autosomes (A) for male and female control libraries.

Additional file 2. Genome browser view of remarkable autosomal and X-linked regions displaying sex-specific and non-specific FAIRE-seq and RNA-seq signal. A, D: female-specific regions around the genes ACYPI003071 (uncharacterized protein) and ACYPI001644 (cuticular protein 44). B, E: male-specific regions around the genes ACYPI080359 (uncharacterized protein) and ACYPI081672 (uncharacterized protein). C, F: regions in common between males and females for the genes ACYPI000061 (ATP synthase subunit beta) and ACYPI006656 (molybdate-anion transporter). The RNA-seq and FAIRE-seq signals have been made equal between males and females for each region.

Additional file 7. Protein conservation of the Drosophilaâ s DCC in the pea aphid. Proteic domains percentage of identity between A. pisum homologs of the five proteins composing the DCC of D. melanogaster.

Additional file 6. Protein sequence comparison of the Drosophila’s DCC in the pea aphid. Clustal multiple sequence alignment by MUSCLE (3.8) of A. pisum’s homologs of D. melanogaster DCC. Proteic domains of the Drosophila are represented in full color boxes above the alignments. A. pisum gene names found by BLASTp are indicated in parenthesis.

Additional file 4. Mean FAIRE signal and proportion of X-linked and autosomal genes depending on their expression profile, grouped by sex. Genes have been categorized in four different classes: unexpressed (A, E), male-biased (B, F), female-biased (C, G) and unbiased (D, H) genes between the two sexes based on gene expression data. The mean FAIRE signal has been calculated around each gene class (500Â bp) and in their gene body (scaled), depending on the chromosome type (autosomes in dark color, X chromosome in light color) and depending on the sex (males, top in blue and females, bottom in red. 99% CI based on bootstraps is also shown around the mean.

Additional file 5. GO enrichment of biological processes for autosomal and X-linked, male- and female-biased genes.

Additional file 3. Mean FAIRE coverage calculated for all autosomal genes (left, black) and X-linked genes (right, gray) for males (blue) and females (red). 99% CI based on 1000 bootstrap is shown around the mean. The FAIRE coverage has been normalized by read-depth in order to allow the comparison between males and females data.