Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution

Abstract

Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes.

Fig. 1.

Evolutionary strata on the emu sex chromosomes. (A) Female and male coverage along the Z chromosome (dots represent individual scaffolds, the lines a sliding window of 10 scaffolds). (B) Female/male SNP densities for emu transcripts, ordered along the chicken Z chromosome, using a sliding window of 10 genes. Putative differentiated regions are colored in yellow (Str0: stratum 0 and Str1: stratum 1), and pseudoautosomal regions are in green (PAR). The red vertical line indicates the location of dmrt1.

Fig. 2.

(A) Synteny and evolutionary strata on the bird Z. Dot plot between Anolis chromosome 2 and the chicken Z chromosome. Dashed lines indicate the position of Z-linked genes in chicken that also have W-linked homologs; these genes have been used to infer the location of three evolutionary strata on the chicken Z (old strata I–III). Regions in yellow are fully differentiated on the emu Z, and the orange region is a more recently differentiated region. The yellow region supposedly corresponds to the ancestral sex-determining segment shared by all birds but contains no remaining W homologs in chicken and can thus not be dated based on Z-W divergence. We refer to this ancestral sex-linked region as stratum 0. The red line gives the location of dmrt1, the ancestral sex-determining gene in birds. (B) Schematic comparison of the chicken and emu Z chromosomes, with the emu differentiated (in yellow) and pseudoautosomal regions (green) colored on the chicken Z. DMRT1 has been mapped to the differentiated region of the emu Z chromosome using in situ hybridization.

Fig. 3.

Patterns of gene expression in emus. Genes were assigned to different chromosomes according to their location in the chicken genome. (A) Log2(female/male FPKM) for the different emu chromosomes at 15 and 42 d. (B) Log2(female/male FPKM) along the Z chromosome using a sliding window of 10 genes at 15 d and 42 d. (C) Log2(male FPKM/female FPKM) at day 15 and 42 on the autosomes, the differentiated regions (stratum 0 and stratum 1), and the pseudoautosomal region (PAR) of the Z chromosome. The dashed lines indicate the median values for each sample.