Drcd-1 related: a positively selected spermatogenesis retrogene in Drosophila

Abstract

Gene duplication is a major force driving genome evolution, and examples of this mode of evolution and of the functions of duplicated genes are needed to reveal general patterns. Here, our study focuses on a particular retrogene (i.e., CG9573) that originated about 5-13 million years ago that we have named Drcd-1 related. It originated in Drosophila through retroposition of the parental gene Required for cell differentiation 1 of Drosophila (Drcd-1; CG14213), which is a known transcription cofactor. Drcd-1r is only present in D. melanogaster, D. simulans, D. sechellia, and D. mauritiana. Drcd-1r is an X to autosome retroposition event. Many retrogenes are X to autosome copies and it has been shown that positive selection underlies this bias. We sought to understand Drcd-1r mode of evolution and function to contribute to the understanding of the selective pressures acting on X to autosome retrogenes. Drcd-1r overlaps with another gene, it is within the 3' UTR of the gene CG13102 and is encoded in the opposite orientation. We have studied the characteristics of the transcripts and quantified expression of CG13102 and Drcd-1r in wild-type flies. We found that Drcd-1r is transcribed specifically in testes. We also studied the molecular evolution of Drcd-1r and Drcd-1 and found that the parental gene has evolved under very strong purifying selection but the retrogene has evolved very rapidly (Ka/Ks ~1) under both positive and purifying selection, as revealed using divergence and polymorphism data. These results indicate that Drcd-1r has a novel function in the Drosophila testes. To further explore Drcd-1r function we used a strain containing a P element inserted in the region where CG13102 and Drcd-1r are located that shows recessive male sterility. Analysis of this strain reveals the difficulties that can be encountered in studying the functions of genes with overlapping transcripts. Avenues for studying of the function of this gene are proposed.

Fig. 1

Drcd-1r genomic region. The genomic organization of the region where Drcd-1r is inserted is shown as annotated in FlyBase. The location of the P element insertion of line 11773 is also shown

Fig. 2

RT-PCR results are shown. The first lane is always the ladder, the second lane is RT+, the third lane is an RT- control and the fourth lane is a PCR negative control. a, b, c and d correspond to CG13102 results using RNA from testis of wild-type males, carcasses from wild-type males, testis from sterile males and carcasses from sterile males, respectively. e, f, g and h correspond to Drcd-1r results using RNA from testis of wild-type males, carcasses from wild-type males, testis from sterile males and carcasses from sterile males, respectively

Fig. 3

dsRNA detection results are shown. a and b correspond to wildj-type and infertile male assays in the 5′ region of overlap. Lane 1 corresponds to the ladder. Lane 2 corresponds to RT+ treated with RNase and denatured. Lane 3 corresponds to RT− treated with RNase and denatured. Lane 4 corresponds to RT+ treated with RNase and not denatured. Lane 5 is the negative control for PCR

Fig. 4

For Drcd-1r and its parental gene (Drcd-1), species and gene phylogeny used by PAML is shown. Nodes and tips are labeled to help interpret Table 1