MOESM2 of Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid

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

Genotype data used for genome scans and construction of genetic maps

The Excel sheet entitled "Genotype_genome_scan" contains the genotypes of 109 individuals at 436 microsatelitte markers used for genome scan analyses. The Excel sheet entitled "Genotype_genetic_map" contains genotype data at 343 polymorphic microsatelitte markers on a 3-generation pedigree that have been used to construct genetic maps

Theoretical predictions of the genomic location of sex-biased genes in aphids.

<p>The preferred chromosomal locations of sexually antagonistic mutations (Prediction 1) are based on the simulations presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003690#pgen-1003690-g002" target="_blank">Figure 2</a>. Prediction 2: Predicted evolution of expression pattern of a gene bearing a sexually antagonist mutation after the evolution of a modifier that reduces the expression in the harmed sex (M, F and A refer to male, sexual female and asexual female, respectively, and the sign represents relative expression in each morph). The genomic locations of sex-biased genes (Predictions 3) were obtained by combining Predictions1 and 2. Theoretical predictions 3 were then tested with empirical data by looking at the genomic location of sex-biased genes, when considering different levels of fold-change in expression (2-, 5-, 10-fold difference). Observed number of genes for X and autosomes, frequency of X-linkage, % deviation from random expectation of X-linkage (<i>f</i>_(X) = 0.12) and its significance (Chi-square tests) are also given.</p

Chromosomal location of genes differentially expressed between reproductive morphs.

<p>Frequency of X-linkage for genes with different rate of expression among males, sexual females and asexual females. Genes were classified according to their pattern of expression (M, F and A stand for male, sexual female and asexual female, respectively, and the sign represents relative expression in each morph) considering different minimal fold-change in expression between reproductive morphs (2-, 5- and 10-fold). The black line shows the expected frequency of X-linkage (based on genes supported by at least 5 reads over the eight libraries). Significance for deviation from the random expectation was calculated with Chi2-tests (* : <i>p</i><0.05, **: p<0.01, *** : <i>p</i><0.001). Theoretical predictions for the preferred genomic location of these different classes of genes (derived under the hypothesis that the evolution of sex-biased gene expression to restrict the product of a sexually antagonistic allele to the sex it benefits might solve intra-locus sexual conflicts) are shown on the top of the figure.</p

Reproductive phenotype of F2 and F3 individuals according to their genotype in the candidate region.

<p>Given are the number of lineages determined as OP, the number of lineages phenotyped, and the percentage of OP lineages (in brackets). <i>op1</i> and <i>op2</i> alleles correspond to the alleles inherited from the L21V1 grandparent clone (OP phenotype). The four different alleles inherited from the two CP grandparents JML06 (alleles <i>CP1</i> and <i>CP2</i>) and LSR1 (<i>CP3</i> and <i>CP4</i>) were aggregated as “<i>CP</i>” since we did not observe differences of reproductive phenotype for the four different CP alleles (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004838#pgen.1004838.s001" target="_blank">Fig. S1</a> for detailed information for each allele).</p>a<p>Progeny in these crosses was selected based on genotype at the candidate locus.</p><p>Reproductive phenotype of F2 and F3 individuals according to their genotype in the candidate region.</p

Model of the effects on fitness (<i>w</i>) of a mutation.

<p><i>s_f</i>, <i>s_m</i> and <i>s_a</i> respectively denote the homozygous or hemizygous effect of a mutation <i>B</i> present in sexual females, males or asexual females, while <i>h_f</i>, <i>h_m</i> and <i>h_a</i> denote the dominance coefficients of <i>B</i> in these different types of individuals.</p

Outlier loci identified by genome scans.

<p>Outlier loci detected with ARLEQUIN 3.5 at α = 0.01 in a hierarchical analysis in which geographical populations were nested within group of populations experiencing selection for the same reproductive mode (OP <i>vs</i> CP). <i>F_CT</i> between CP and OP populations (and significance as outlier) are shown, as well as expected heterozygosity (<i>H_E</i>). Outlier detection analyses were also performed among OP and CP populations to ensure these loci were not outlier at this hierarchical level. The position on chromosomes is also given.</p><p>Outlier loci identified by genome scans.</p

Annual life-cycle of the pea aphid and ploidy levels for autosomes (A) and sex-chromosome (X).

<p>Overwintering egg, diploid for both types of chromosomes (AA and XX) gives birth to an asexual female. After several cycles of apomictic parthenogenesis, asexual females produce sexual females and males. Males inherit the same autosomal genome as asexual females, but receive only one of the female Xs: hence they are diploid for the autosomes and haploid for the X (represented as AAX0). Ovules (haploid for both the autosomes and the X) are generated by a normal meiosis, but males produce only X-bearing sperm (AX). The fusion of male and female gametes restores the diploid level at both the X and the autosomes.</p

Simulation of the accumulation of sexually antagonistic mutations on X chromosome and autosomes in aphids.

<p>Characteristics of mutations (in terms of their selection coefficients in males [<i>s_m</i>], in sexual females [<i>s_f</i>] and in asexual females [<i>s_a</i>]) that rise in frequency on the X more than on autosomes (panel A) or <i>vice-versa</i> (panel B) as a function of the dominance coefficient <i>h</i>. Our simulations predict that the X chromosome of aphids should be enriched in sexually antagonistic alleles beneficial for males whereas autosomes should be enriched in alleles favorable for asexual females under all dominance values.</p

Expression rate of X-linked and autosomal genes in males, sexual females and asexual females.

<p>Panels A to C: Log2 expression (RPKM+1) for autosomal and X-linked genes in the different reproductive morphs (males, sexual females, asexual females) for different cut-offs in gene expression. The white box for males represents X-linked genes with doubled expression to account for the haploid state of X chromosome in males. Difference in gene expression between X and autosomes within each morph was tested with Wilcoxon Rank sum tests.</p