Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition

Abstract

In birds, as in mammals, one pair of chromosomes differs between the sexes. In birds, males are ZZ and females ZW. In mammals, males are XY and females XX. Like the mammalian XY pair, the avian ZW pair is believed to have evolved from autosomes, with most change occurring in the chromosomes found in only one sex--the W and Y chromosomes. By contrast, the sex chromosomes found in both sexes--the Z and X chromosomes--are assumed to have diverged little from their autosomal progenitors. Here we report findings that challenge this assumption for both the chicken Z chromosome and the human X chromosome. The chicken Z chromosome, which we sequenced essentially to completion, is less gene-dense than chicken autosomes but contains a massive tandem array containing hundreds of duplicated genes expressed in testes. A comprehensive comparison of the chicken Z chromosome with the finished sequence of the human X chromosome demonstrates that each evolved independently from different portions of the ancestral genome. Despite this independence, the chicken Z and human X chromosomes share features that distinguish them from autosomes: the acquisition and amplification of testis-expressed genes, and a low gene density resulting from an expansion of intergenic regions. These features were not present on the autosomes from which the Z and X chromosomes originated but were instead acquired during the evolution of Z and X as sex chromosomes. We conclude that the avian Z and mammalian X chromosomes followed convergent evolutionary trajectories, despite their evolving with opposite (female versus male) systems of heterogamety. More broadly, in birds and mammals, sex chromosome evolution involved not only gene loss in sex-specific chromosomes, but also marked expansion and gene acquisition in sex chromosomes common to males and females.

Figure 1. The Z Amplicon

a. Fluorescence in situ hybridization of Z-amplicon BAC CH261-77N6 (red) to distal long arm of Z chromosome (blue). b. Z amplicon (red) comprises most distal 11 Mb of Z chromosome. c. Triangular dot plots each comparing the sequence of a Z-chromosome BAC to itself. Within the plot, each dot represents a perfect match of 50 base pairs. Direct repeats appear as horizontal lines; scale bar represents 50kb. On left, BAC CH261-73L15 contains six tandem repeats covering 120 kb immediately proximal to Z amplicon. On right, BAC CH261-137P21, a representative Z amplicon clone. Each 25–30kb repeat unit is ~95% similar to any other, though some units have been disrupted by insertions and deletions. d. Genes in repeat units of Z amplicon; scale bar represents 5kb. Each 20kb repeat unit of small array in CH261-73L15 contains one copy of ADCY10z. Each 25–30kb repeat unit of Z amplicon contains one copy each of C2ORF3z, MRPL19z, and RICSz. e. RT-PCR analysis of Z-amplicon gene expression in adult tissues. HPRT1 is widely expressed in adult tissues and serves as positive control for reverse transcriptase reaction. All Z-amplicon genes are expressed in testis, but not other tissues.

Figure 2. Independent origin of chicken Z and human X chromosomes

Rectangular dot plots show chromosomal locations of Z-orthologous or X-orthologous genes in other species. a. Chicken Z chromosome versus selected human chromosomes. Chicken Z chromosome is not orthologous to human X, but is orthologous to portions of human autosomes 5 (yellow), 9 (blue), and 18 (purple). At right: three-color projection of dot plots onto a unified schematic of chicken Z, showing that orthology to human chromosomes 5, 9, and 18 accounts for most of Z chromosome, with exception of Z amplicon on distal long arm. b. Human X chromosome versus selected chicken chromosomes. Human X chromosome is not orthologous to chicken Z, but is orthologous to portions of chicken autosomes 1 (red) and 4 (cyan). At right: two-color projection of dot plots onto unified schematic of human X, showing that orthology to chicken chromosomes 1 and 4 spans X (colored bar). c. Chicken Z chromosome (orange) and human X chromosome (green) versus selected stickleback chromosomes. Chicken Z and human X orthologs occupy separate and distinct locations within stickleback genome. Chicken Z orthologs are present on stickleback chromosomes 13 and 14, while human X orthologs are present on stickleback chromosomes 1, 4, 7, and 16.

Figure 3. Convergent gene gain on the chicken Z and human X chromosomes

a. Gene density of Z and X chromosomes compared to autosomes. Both are unusually gene poor, with about half the gene density of a typical autosome. b. Venn diagrams comparing gene content of chicken Z and human X chromosomes to orthologous autosomes. Most genes on orthologous autosomes remain on the sex chromosomes; few have been lost. Both chicken Z and human X gained hundreds of genes not present on orthologous autosomes. c. Percentage of protein coding genes with testis ESTs in Unigene. Left panel: Compared to chicken autosomes, Z chromosome is enriched for testis-expressed genes. Single-copy Z chromosome genes (SC) show no enrichment for testis ESTs compared to autosomal gene, but nearly all multi-copy (MC) genes are expressed in testis. Right panel: Similar results on human X chromosome.