Demasculinization of X chromosomes in the Drosophila genus

Abstract

X chromosomes evolve differently from autosomes, but general governing principles have not emerged. For example, genes with male-biased expression are under-represented on the X chromosome of D. melanogaster, but are randomly distributed in the genome of Anopheles gambiae. In direct global profiling experiments using species-specific microarrays, we find a nearly identical paucity of genes with male-biased expression on D. melanogaster, D. simulans, D. yakuba, D. ananassae, D. virilis and D. mojavensis X chromosomes. We observe the same under-representation on the neo-X of D. pseudoobscura. It has been suggested that precocious meiotic silencing of the X chromosome accounts for reduced X chromosome male-biased expression in nematodes, mammals and Drosophila. We show that X chromosome genes with male-biased expression are under-represented in somatic cells and in mitotic male germ cells. These data are incompatible with simple X chromosome inactivation models. Using expression profiling and comparative sequence analysis, we show that selective gene extinction on the X chromosome, creation of new genes on autosomes and changed genomic location of existing genes contribute to the unusual X chromosome gene content.

Figure 1. Genes that show sex-biased expression, on chromosome arms

a, Percentage of genes with female-biased (red), non-biased (grey) and male-biased (blue) expression on chromosome arms. Muller's elements and arms are indicated (X chromosomes in bold). Significant under-representation from a random distribution of genes in an expression class (chi-squared test) is noted (*P<10⁻⁴). The top 20% of differentially expressed genes (by ranked P values) are assigned a sex-biased expression class. b, Box plots of average hybridization intensities for males by chromosome arm. Twenty-fifth to seventy fifth percentiles (boxes), medians (lines in boxes) and ranges (whiskers) are indicated. c, As in a, but with genes with predicted testis-biased expression removed. D. melanogaster, D. mel; D. simulans, D. sim, D. yakuba, D. yak; D. ananassae, D. ana; D. pseudoobscura, D. pse; D. virilis, D. vir; D. mojavensis, D. moj.

Figure 2. Male-biased expression not subject to X chromosome inactivation

a–c, Percentage of D. melanogaster genes with male-biased expression. Significant under-representation as in Fig. 1 is noted (*P<10⁻²; **P<10⁻⁴). a, Non-gonadal soma (gonadectomized carcasses). b, c, Testis from mutants with mitotically active germline tumours. Male-biased expression was determined by present calls in wild-type and mutant testis and absent calls in wild-type ovary expression profiles from FlyMine. Testis from bgcn⁻ males (primary spermatocyte-biased; b) accumulates mitotically active cysts of interconnected germ cells, whereas testis from males overexpressing os (nos-os) in a bgcn⁻ background (male germline stem-cell-biased; c) accumulates mitotically active germ cells that undergo complete cytokinesis. d–f, Box plots of average intensities (arbitrary scale) across hybridizations for wild-type (d), bgcn⁻ (e), or nos-os; bgcn⁻ (f) testis separated by chromosome arm. Twenty-fifth to seventy-fifth percentiles (boxes), medians (lines in boxes) and ranges (whiskers) are indicated.

Figure 3. The neo-X chromosome

a, D. pseudoobscura neo-X chromosome formation cartoon. Muller A, D and E are attached to different centromeres (filled circles) in D. pseudoobscura relative to flanking species. b, Bar plot showing changes to D. pseudoobscura Muller D neo-X chromosome (orange) and Muller E autosomal arm (green), based on the predicted expression pattern of the ancestral autosomes. Categories are: switches in sex-biased expression (F, female-biased; M, male-biased), not found (absent), only found in D. pseudoobscura (new), and genes moving from (move off) and to (move on) the indicated arm. Significant differences (chi-squared test) between Muller D and Muller E are noted (**P<10⁻⁴; *P<0.05). The ancestral condition of the neo-X chromosome was inferred by examining chromosome linkage and expression on homologous arms in species that diverged from the Drosophila lineage before and after D. pseudoobscura.