Positive selection for the male functionality of a co-retroposed gene in the hominoids

We tackled these problems by analyzing the evolutionary signature in both within-species variation and between species divergence in the sequence and structure of the gene. We revealed a significant evolutionary signature: the coding region has significantly lower sequence variation, especially insertions and deletions, suggesting that the human copy may encode a protein. Moreover, a survey across five different hominoid species revealed that all adaptive changes of PSMD4-derived regions occurred on branches leading to human and chimp rather than other hominoid lineages. Finally, computational analysis suggests testis-specific transcription of PIPSL is regulated by tissue-dependent methylation rather than some transcriptional leakage.Therefore, this set of analyses showed that PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in the male functions of humans and its close relatives.Retroposition, an RNA-intermediated copy mechanism, could shape genomes widely in eukaryotes, and in particular plays a substantial role in evolution of functional novelties [1]. People ever viewed it as a trivial molecular process for making functionless processed pseudogenes [2]. However, extensive analyses have revealed that a large number of retrosequences have acquired various functions from vertebrates to invertebrates [3,4], from spermatogenesis [3] to courtship behaviors [5]. Many retrogenes could recruit nearby preexisting exon-intron sequences and genomic regions to form a chimeric gene structure with novel protein structures, which may expand protein functional diversity [6-8].Almost all observed retroposition events involve a single parental gene that serves as substrate for retroposition. However, Akiva et al recently observed an extraordinary case that two adjacent genes in the hominoid lineage, PIP5K1A and PSMD4 in chromosome 1, co-retroposed from a read-through transcript and formed a new chimeric gene, PIPSL, in chromosome 10 [9]. PIP5K1A enc