Gene-by-Gene or Localized Dosage Compensation on the Neo-X Chromosome in Drosophila miranda

Abstract

Many organisms have a global mechanism for dosage compensation (DC) operating along the entire male X chromosome, which equalizes gene expression on the male X with that on the two Xs in females and/or on autosomes. At the initial stage of sex chromosome evolution, however, gene-by-gene (or localized) DC may also be necessary because the degeneration of Y-linked genes occurs independently at different times. We therefore tested whether the up-regulation of X-linked genes depends on the status of their Y-linked homologs, using the young sex chromosomes, neo-X and neo-Y, in Drosophila miranda. In support of the presence of gene-by-gene DC, the extent of up-regulation in males was indeed higher for neo-X-linked genes with pseudogenized neo-Y-linked homologs than for neo-X-linked genes with functional neo-Y-linked homologs. Further molecular evolutionary analysis also supports the idea that many individual neo-X-linked genes first acquired the potential for up-regulation, which then enabled the pseudogenization of neo-Y-linked homologs, without serious deleterious effects on male fitness.

Fig. 1.

—Relationship between the functionality of neo-Y-linked genes and the extent of DC on neo-X-linked genes in the thorax, testis, abdomen without gonad, and abdomen (from left to right). X_F–Y_F, a group of genes for which both neo-X-linked and neo-Y-linked homologs are functional; X_F–Y_P, a group of genes for which neo-X-linked homologs are functional, but neo-Y-linked homologs are pseudogenized. The numbers of genes analyzed are 461 and 757 for the X_F–Y_F and X_F–Y_P genes, respectively. The lines in the boxes represent medians, 50% of values are included in the boxes, and 80% of values are included within the bars. Differences in median values between groups were tested based on a Monte-Carlo simulation with 1,000 bootstrap replicates: ***, P < 0.001. A solid line indicates the R_Lin value of 1, indicating perfect DC, whereas a broken line corresponds to a value of 0.5, indicating no DC. + below each bar means that the median R_Lin value is significantly >0.5 at the 5% significance level.

Fig. 2.

—Relationship between the relative time after pseudogenization of neo-Y-linked genes and the extent of dosage compensation (DC) on the neo-X-linked homologs. The R_Lin values in a tissue where each gene is expressed most highly among the tissues examined were used. The lines in the boxes represent medians, 50% of values are included in the boxes, and 80% of values are included within the bars. Solid and broken lines correspond to the R_Lin value of 1 and 0.5, respectively. Differences in median values between groups were tested based on a Monte-Carlo simulation with 1,000 bootstrap replicates; P ≥ 0.05 for all pairwise comparisons. The number of genes analyzed for each category is shown in parentheses.

Fig. 3.

—Expression patterns and pseudogenization of neo-Y-linked genes. (A) Relationship between genes showing maximum expression in various tissues and the proportion of functional genes. Gene expression based on cFPKM (see Materials and Methods) in Drosophila pseudoobscura was used as a proxy for the ancestor without neo-sex chromosomes. (B) Relationship between the functionality of neo-sex-linked genes and the proportion of genes with the highest expression in the testis or accessory gland. X_F–Y_F, for genes that are functional on both neo-X and neo-Y; X_F–Y_P, for genes that are functional on the neo-X, but pseudogenized on the neo-Y; X_P–Y_F, for genes that are pseudogenized on the neo-X, but functional on the neo-Y; and X_P–Y_P, for genes that are pseudogenized on both the neo-X and neo-Y. Error bars showing the 95% confidence interval and statistical significance were calculated based on a Monte-Carlo simulation with 1,000 bootstrap replicates: ***, P < 0.001; *, P < 0.05; NS, P ≥ 0.05. The number of genes analyzed for each category is shown in parentheses.