Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators

Abstract

After birds diverged from mammals, different ancestral autosomes evolved into sex chromosomes in each lineage. In birds, females are ZW and males are ZZ, but in mammals females are XX and males are XY. We sequenced the chicken W chromosome, compared its gene content with our reconstruction of the ancestral autosomes, and followed the evolutionary trajectory of ancestral W-linked genes across birds. Avian W chromosomes evolved in parallel with mammalian Y chromosomes, preserving ancestral genes through selection to maintain the dosage of broadly expressed regulators of key cellular processes. We propose that, like the human Y chromosome, the chicken W chromosome is essential for embryonic viability of the heterogametic sex. Unlike other sequenced sex chromosomes, the chicken W chromosome did not acquire and amplify genes specifically expressed in reproductive tissues. We speculate that the pressures that drive the acquisition of reproduction-related genes on sex chromosomes may be specific to the male germ line.

Figure 1. Structure of chicken W chromosome

(a) Sequence map of W chromosome, covering 7 Mb in 13 contigs. (b) 28 protein-coding genes. See also Supplementary Data 2 and Supplementary Data 3. (c) Clone map; highlighted clones (red) were used as probes in lampbrush FISH. See also Supplementary Table 1 and Supplementary Data 1. (d) Radiation hybrid retention frequencies for single-copy markers (orange circles) and the average for each chromomere (dashed lines). Chromomere 4, located near centromere, displays highest average retention frequency. See also Supplementary Data 4. (e) Schematic representation of W chromosome at diplotene of female meiosis. The pseudoautosomal region (green) contains chiasma between terminal giant lumpy loops (TGL) at W and Z termini. Chromomeres numbered in ascending order from free end of W chromosome to chiasma region. Heterochromatic repeat families (red-hashes) occupy chromomeres 1, 3, 5, and 6. Chromomeres 2, 4, and 7 correspond to three distinct radiation hybrid linkage groups; most of their sequence is ancestral single-copy sequence (yellow); small ampliconic region (blue) contains HINTW. See also Supplementary Fig. 2. (f) Lampbrush FISH localizes BAC probes from each RH linkage group to a different chromomere. The TGL site is marked with green arrowhead; each chromomere is numbered in white. Scale bar 5 μm. BAC probes contain interspersed repeats and give weak secondary signals at multiple sites on the W and other chromosomes; primary signal marked with white arrowhead. CH261-75N4 (red) localizes to chromomere 2, CH261-107E4 (red) to chromomere 4, and CH261-114G22 (red) to chromomere 7. See also Supplementary Fig. 1.

Figure 2. Chicken W chromosome genes are broadly expressed across adult somatic tissues

Heatmap showing relative expression levels of W chromosome genes in adult female tissues from the Chickspress RNA-seq dataset (PRJNA204941). Each gene is normalized to the highest expressing tissue.

Figure 3. Ancestral Z-W gene pairs from 14 avian species

(a) Phylogenetic tree of species in this study, with branches colored to highlight relationships among species. Humans diverged from birds (yellow) 325 MYA (million years ago). Green anole lizard and American alligator diverged from birds 275 and 219 MYA, and were used to resolve gene gains and losses between birds and mammals. Birds diverged from each other starting around 120 MYA (yellow). Branches of major avian linages are shaded: galloanserae (green), neoaves (purple), and paleognathae (red). (b) Euler diagram showing overlapping sets of ancestral Z-W gene pairs identified in chicken (dark pink); four species (chicken, collared flycatcher, crested ibis, and emu) (medium pink); and all 14 published female avian genomes (light pink), as subsets of all 685 ancestral Z genes (light yellow). See also Supplementary Table 3.

Figure 4. Factors in the survival of Z-W gene pairs

Violin plots, with median (black circle) and interquartile range (black bar), comparing annotations of ancestral Z-W gene pairs identified in chicken (dark pink); four species (chicken, collared flycatcher, crested ibis, and emu) (medium pink); and all 14 published female avian genomes (light pink), versus remainder of ancestral Z genes (light yellow). P values obtained using one-tailed Mann-Whitney U test. See Statistics and Supplementary Fig. 3. (a) Human orthologs of ancestral Z-W pairs have higher probability of haploinsufficiency than other ancestral Z genes. Chicken P < 5.8 ×10⁻⁵; four species P < 1.6 ×10⁻³; 14 species P < 8.34 ×10⁻⁴. (b) Chicken Z orthologs of ancestral Z-W pairs are more broadly expressed in adult chicken tissues than other ancestral Z genes. Chicken P < 2.1 ×10⁻³; four species P < 3.8 ×10⁻³; 14 species P < 0.059. (c) Chicken Z orthologs of ancestral Z-W pairs are more highly expressed in chicken blastocysts. Chicken P < 7.7×10⁻⁷; four species P < 1.1 ×10⁻³; 14 species P < 2.8 ×10⁻³. (d) Chicken Z orthologs of ancestral Z-W pairs have reduced ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (dN/dS) in alignments with orthologs in duck. Chicken P < 0.022; four species P < 0.052; 14 species P < 3.6 ×10⁻³. (e) Collared flycatcher. Chicken P < 8.6×10⁻⁵; four species P < 7.7 ×10⁻⁵; 14 species P < 2.9 ×10⁻⁵. (f) Zebra finch. Chicken P < 9.5×10⁻⁵; four species P < 1.3 ×10⁻⁴; 14 species P < 1.6 ×10⁻⁴.

Figure 5. Regulatory annotations of chicken ancestral Z-W pairs

Euler diagram depicting regulatory functions predicted for selected Z-W pair genes on basis of UniProt annotations of human ortholog. See also Supplementary Table 4.