Abstract
Since the two eutherian sex chromosomes diverged from an ancestral autosomal pair, the X has remained relatively gene-rich, while the Y has lost most of its genes through the accumulation of deleterious mutations in nonrecombining regions. Presently, it is unclear what is distinctive about genes that remain on the Y chromosome, when the sex chromosomes acquired their unique evolutionary rates, and whether X-Y gene divergence paralleled that of paralogs located on autosomes. To tackle these questions, here we juxtaposed the evolution of X and Y homologous genes (gametologs) in eutherian mammals with their autosomal orthologs in marsupial and monotreme mammals. We discovered that genes on the X and Y acquired distinct evolutionary rates immediately following the suppression of recombination between the two sex chromosomes. The Y-linked genes evolved at higher rates, while the X-linked genes maintained the lower evolutionary rates of the ancestral autosomal genes. These distinct rates have been maintained throughout the evolution of X and Y. Specifically, in humans, most X gametologs and, curiously, also most Y gametologs evolved under stronger purifying selection than similarly aged autosomal paralogs. Finally, after evaluating the current experimental data from the literature, we concluded that unique mRNA/protein expression patterns and functions acquired by Y (versus X) gametologs likely contributed to their retention. Our results also suggest that either the boundary between sex chromosome strata 3 and 4 should be shifted or that stratum 3 should be divided into two strata.
Highlights
Therian sex chromosomes, X and Y, evolved from a pair of homologous autosomes and originally harbored an identical set of genes [1,2,3]
By utilizing whole-genome transcriptome and other published experimental data, we examined whether the expression and functional divergence of Y from X gametologs correlated with their evolution and potentially contributed to their survival on the sex chromosomes
We observed that immediately following the suppression of recombination between X and Y, likely due to their importance in both sexes, X gametologs largely maintained the ancestral autosomal sequence and functional constraints
Summary
Therian sex chromosomes, X and Y, evolved from a pair of homologous autosomes and originally harbored an identical set of genes [1,2,3]. There are several proposed scenarios for how paralogs diverge from one another, including asymmetric evolution, where one copy is presumed to maintain the ancestral function, and experiences stronger purifying selection, while the other copy can undergo neofunctionalization or pseudogenization [12] and might experience positive selection or evolve neutrally. If this scenario holds true with respect to X and Y divergence, we expect that X gametologs will maintain the ancestral somatic functions necessary to both males and females (because the X is present in both sexes), and will evolve under purifying selection. Similar to paralogs, divergence in function and expression between Y- and X-gametologs might contribute to the survival, in
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