Abstract
The formation of new genes is a primary driving force of evolution in all organisms. The de novo evolution of new genes from non-protein-coding genomic regions is emerging as an important additional mechanism for novel gene creation. Y chromosomes underlie sex determination in mammals and contain genes that are required for male-specific functions. In this study, a search was undertaken for Y chromosome de novo genes derived from non-protein-coding sequences. The Y chromosome orphan gene variable charge, Y-linked (VCY)2, is an autosome-derived gene that has sequence similarity to large autosomal fragments but lacks an autosomal protein-coding homolog. VCY2 locates in the amplicon containing long DNA fragments that were transposed from autosomes to the Y chromosome before the ape-monkey split. We confirmed that VCY2cannot be encoded by autosomes due to the presence of multiple disablers that disrupt the open reading frame, such as the absence of start or stop codons and the presence of premature stop codons. Similar observations have been made for homologs in the autosomes of the chimpanzee, gorilla, rhesus macaque, baboon and out-group marmoset, which suggests that there was a non-protein-coding ancestral VCY2 that was common to apes and monkeys that predated the transposition event. Furthermore, while protein-coding orthologs are absent, a putative non-protein-coding VCY2 with conserved disablers was identified in the rhesus macaque Y chromosome male-specific region. This finding implies that VCY2 might have not acquired its protein-coding ability before the ape-monkey split. VCY2 encodes a testis-specific expressed protein and is involved in the pathologic process of male infertility, and the acquisition of this gene might improve male fertility. This is the first evidence that de novo genes can be generated from transposed autosomal non-protein-coding segments, and this evidence provides novel insights into the evolutionary history of the Y chromosome.
Highlights
The emergence of new genes with novel functions is important for adaptive evolutionary innovation [1]
15 de novo protein-coding genes have identified in the ancestral primate genome using comparative genomic analyses [16], while other studies have found three putative protein-coding genes in humans and 11 novel genes in the murine genome [17,18], and de novo protein-coding genes involved in brain function [19] and with tumor-specific expression have been identified [20]
If a protein-coding gene in the Xdegenerate region had been generated de novo from a proto-X/Y sequence, non-proteincoding copies would be found on chromosome X (Chr-X) (Fig. 1B)
Summary
The emergence of new genes with novel functions is important for adaptive evolutionary innovation [1]. It has recently become apparent that new genes can arise de novo from nonprotein-coding DNA; examples have been reported in fruit flies (Drosophila) [3,4,5,6,7,8], ants and other insects [9], budding yeast (Saccharomyces cerevisiae) [10,11,12], rice (Oryza sativa) [13], protozoal parasite Plasmodium vivax [14], mice (Mus musculus) [15], primates, and humans. There have been no such reports of de novo protein-coding genes on the Chr-Y, which harbors genes for male-specific functions
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