Genes copies may arise by retrotransposition, in which the mRNA of a parental gene is reverse transcribed and re-inserted into the genome. As these retrocopies are mRNA-derived, they characteristically lack the introns and flanking sequence of their parental genes. A number of independent studies, at both single gene and genome-wide levels, have sought to identify protein coding genes derived by retrotransposition.
In this FlyBase analysis, the results of various publications were collected to identify a well supported set of retrotransposed protein coding genes. Published abstracts were searched for descriptions of functional protein coding retrocopies of genes in D. melanogaster using queries 'retrogene', 'retroposition' and 'retrotransposition'. This search yielded 685 calls for 420 putative retrotransposed protein coding genes from 22 publications, including seven large lists of putative retrogenes from genome-wide studies, three small lists of putative retrogenes from more focussed genome-wide studies, and 12 single gene papers (see References section below). For each of these 685 calls, a standardized comment with the key words 'derived' and 'retroposition' has been attached to the putative retrotransposed gene that can be found in the 'Other Information > Relationship to Other Genes' section of the gene report. For example: The RpL37b gene may be derived from the RpL37a gene by retroposition.
Additionally, the data were reviewed to identify a set of well supported retrotransposed protein coding genes. In a first pass, genes from small studies, and genes called in at least two different high throughput studies, were selected (n = 202). These first pass genes were then reviewed to confirm a quality alignment between the putative retrogene and a plausible parental gene that confirmed intron loss, substantiating the inference of retrotransposition. Calls from two genome-wide studies (Langille and Clark, 2007 and Zhang et al., 2011) were accepted as their alignment methods were careful to ensure that the aligned region spanned a lost intron (confirmed by sampling of these calls). Calls from other genome-wide studies were less stringent - specifically, pairs of similar genes were reported in which only one of the pair lacked introns, without confirmation that the alignment between the two spanned an exon junction in the parental gene - such that partial DNA-based duplication could not be ruled out as an alternative to retroposition. As such, first pass genes not reported in the two aforementioned higher quality genome-wide studies were curator-reviewed using manual BLAST alignments. Putative retrogenes with conflicting parental gene assignments, or different retrogenes sharing the same parental gene assignment, were also curator-reviewed. Retrogenes for which no specific parental gene was reported in the study were rejected. A total of 142 genes were accepted in the second pass, to which the SO term 'retrotransposed_protein_coding_gene' was appended. These attached terms can be found in the 'Gene Model and Products > Sequence Ontology: Class of Gene' section of the gene report. All calls and subsequent FlyBase analysis are presented in the associated spreadsheet, FB_retrogenes.2014.8.5.xlsx.
Large retrogene sets:
Betran et al., 2002, Genome Res. 12(12): 1854--1859 Retroposed new genes out of the X in Drosophila.
Bai et al., 2007, Genome Biol. 8(1): R11 Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila.
Dai et al., 2006, Gene 385: 96--102 Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes.
Langille and Clark, 2007, Genomics 90(3): 334--343 Parent genes of retrotransposition-generated gene duplicates in Drosophila melanogaster have distinct expression profiles.
Zhang et al., 2010, Genome Res. 20(11): 1526--1533 Age-dependent chromosomal distribution of male-biased genes in Drosophila.
Zhang et al., 2011, Bioinformatics 27(13): 1749--1753 A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes.
Pan and Zhang, 2009, PLoS ONE 4(3): e5040 Burst of young retrogenes and independent retrogene formation in mammals.
Small retrogene sets:
Metta and Schlötterer, 2010, BMC Evol. Biol. 10: 114 Non-random genomic integration - an intrinsic property of retrogenes in Drosophila?
Croset et al., 2010, PLoS Genet. 6(8): e1001064 Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction.
Miskei et al., 2011, PLoS ONE 6(7): e22218 Molecular evolution of phosphoprotein phosphatases in Drosophila.
Single retrogene studies:
Betran et al., 2006, Mol. Biol. Evol. 23(11): 2191--2202 Fast protein evolution and germ line expression of a Drosophila parental gene and its young retroposed paralog.
Charles et al., 1997, Genetics 147(3): 1213--1224 A cluster of cuticle protein genes of Drosophila melanogaster at 65A: sequence, structure and evolution.
Currie and Sullivan, 1994, Genetics 138(2): 353--363 Structure, expression and duplication of genes which encode phosphoglyceromutase of Drosophila melanogaster.
Kalamegham et al., 2007, Mol. Biol. Evol. 24(3): 732--742 Drosophila mojoless, a retroposed GSK-3, has functionally diverged to acquire an essential role in male fertility.
Krasnov et al., 2005, Nucleic Acids Res. 33(20): 6654--6661 A retrocopy of a gene can functionally displace the source gene in evolution.
Li et al., 2011, BMC Evol. Biol. 11: 337 A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits.
Loppin et al., 2005, Curr. Biol. 15(2): 87--93 Origin and neofunctionalization of a Drosophila paternal effect gene essential for zygote viability.
Malmanche et al., 2003, J. Mol. Evol. 56(5): 630--642 The PRAT purine synthesis gene duplication in Drosophila melanogaster and Drosophila virilis is associated with a retrotransposition event and diversification of expression patterns.
Mugue, 2007.2.26, Helping FlyBase: ADRC-60691. Helping FlyBase: ADRC-60691.
Phadnis et al., 2012, Mol. Biol. Evol. 29(5): 1429--1440 Birth, death, and replacement of karyopherins in Drosophila.
Quezada-Díaz et al., 2010, Genetica 138(9-10): 925--937 Drcd-1 related: a positively selected spermatogenesis retrogene in Drosophila.
Steiger et al., 2010, J. Biol. Chem. 285(22): 17089--17097 The Drosophila Copper Transporter Ctr1C Functions in Male Fertility.