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

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

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

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

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

Genomic Analysis of the Necrotrophic Fungal Pathogens <i>Sclerotinia sclerotiorum</i> and <i>Botrytis cinerea</i>

<div><p><i>Sclerotinia sclerotiorum</i> and <i>Botrytis cinerea</i> are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of <i>S. sclerotiorum</i> and two strains of <i>B. cinerea</i>. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the <i>S. sclerotiorum</i> assembly to 16 chromosomes and found large-scale co-linearity with the <i>B. cinerea</i> genomes. Seven percent of the <i>S. sclerotiorum</i> genome comprises transposable elements compared to <1% of <i>B. cinerea</i>. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of <i>B. cinerea</i>–specific secondary metabolites relative to <i>S. sclerotiorum</i>. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between <i>S. sclerotiorum</i> and <i>B. cinerea</i>. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.</p></div