These gene names will be used herein for the orthologous genes in other Drosophila species. melanogaster parent genes are CG4960, CG11825, and Sep5, respectively. melanogaster parent genes are CG8331, CG17734, and Sep2. melanogaster, each consisting of a parent gene and retrogene. To gain insight into the evolution of retrogene expression, we examined three gene pairs that were previously identified in D. Also, if a parent gene’s expression pattern is conserved across species, regardless of whether or not the retrogene is present, then this would suggest that the retrogene has evolved a novel function rather than taking over part of the parent gene’s function via subfunctionalization. Conservation of a retrogene’s expression pattern would indicate an early establishment of function, whereas a lack of conservation would suggest diversification of function. It is unclear whether or not the expression patterns of a parent gene and retrogene are conserved across species.
melanogaster, but many of these putative elements are not conserved in other Drosophila species. Cis-regulatory element prediction has been applied to retrogenes in D. indicated that retrogenes do not typically acquire regulatory elements from their parent genes. An investigation of retrogene regulatory elements in D. melanogaster, suggesting that the loss of parental regulatory elements does not limit the expression of functional retrogenes. The mean expression levels of retrogenes are not significantly different from all genes in D. Expression data from Drosophila melanogaster show that retrogenes tend to be expressed at a lower level and in fewer tissues than their parents, with the exception that retrogenes tend to be more represented in testes than parent genes. Genome-wide studies have provided insights into the evolutionary outcome of this initial asymmetry between parent gene and retrogene regulatory elements and expression patterns, including several studies focusing on protein-coding parent genes and retrogenes in Drosophila.
The lack of parental regulatory elements in a new retrogene is often associated with a lack of function and pseudogenization however, those retrogenes that are transcribed presumably lack the expression pattern of their parents and may therefore acquire novel functions. Retroduplication occurs when mRNA from a parent gene is reverse-transcribed and inserted into the genome, producing a new retrogene copy that lacks the regulatory elements and introns of the parent. Following duplication, gene copies can diverge in function. Gene duplication plays a major role in evolution by expanding gene families and facilitating the diversification of gene function. Therefore, in general, retrogene expression patterns and coding sequences are distinct compared to their parents and, in some cases, retrogene expression patterns diversify. The coding sequences of the three gene pairs appear to be evolving predominantly under negative selection however, the parent genes and retrogenes show some distinct differences in amino acid sequence. We used the genome sequences of 20 Drosophila species to investigate coding sequence evolution. In contrast, expression patterns of the retrogene orthologs have diversified.
Expression patterns of the parent genes and their single copy orthologs are relatively conserved across species, whether or not a species has a retrogene copy, although there is some variation in CG8331 and CG17734. We investigated the embryonic expression patterns of these gene pairs across multiple Drosophila species. To explore the evolution of parent genes and retrogenes, we investigated three such gene pairs in the family Drosophilidae in Drosophila melanogaster, these gene pairs are CG8331 and CG4960, CG17734 and CG11825, and Sep2 and Sep5. It is not clear how a retrogene’s lack of parental regulatory sequences affects the evolution of the gene pair.
Retrogenes form a class of gene duplicate lacking the regulatory sequences found outside of the mRNA-coding regions of the parent gene.