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Citation
dos Santos, G. (2014). Summary of published retrogene analyses. 
FlyBase ID
FBrf0225799
Publication Type
FlyBase analysis
Abstract
PubMed ID
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DOI
Related Publication(s)
Research paper

Origin and neofunctionalization of a Drosophila paternal effect gene essential for zygote viability.
Loppin et al., 2005, Curr. Biol. 15(2): 87--93 [FBrf0183836]

Structure, expression and duplication of genes which encode phosphoglyceromutase of Drosophila melanogaster.
Currie and Sullivan, 1994, Genetics 138(2): 353--363 [FBrf0076544]

A cluster of cuticle protein genes of Drosophila melanogaster at 65A: sequence, structure and evolution.
Charles et al., 1997, Genetics 147(3): 1213--1224 [FBrf0099152]

Retroposed new genes out of the X in Drosophila.
Betran et al., 2002, Genome Res. 12(12): 1854--1859 [FBrf0155820]

The PRAT purine synthesis gene duplication in Drosophila melanogaster and Drosophila virilis is associated with a retrotransposition event and diversification of expression patterns.
Malmanche et al., 2003, J. Mol. Evol. 56(5): 630--642 [FBrf0159078]

A retrocopy of a gene can functionally displace the source gene in evolution.
Krasnov et al., 2005, Nucleic Acids Res. 33(20): 6654--6661 [FBrf0191342]

Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila.
Bai et al., 2007, Genome Biol. 8(1): R11 [FBrf0192134]

Fast protein evolution and germ line expression of a Drosophila parental gene and its young retroposed paralog.
Betran et al., 2006, Mol. Biol. Evol. 23(11): 2191--2202 [FBrf0192808]

Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes.
Dai et al., 2006, Gene 385: 96--102 [FBrf0194437]

Parent genes of retrotransposition-generated gene duplicates in Drosophila melanogaster have distinct expression profiles.
Langille and Clark, 2007, Genomics 90(3): 334--343 [FBrf0200094]

Drosophila mojoless, a retroposed GSK-3, has functionally diverged to acquire an essential role in male fertility.
Kalamegham et al., 2007, Mol. Biol. Evol. 24(3): 732--742 [FBrf0201863]

The Drosophila Copper Transporter Ctr1C Functions in Male Fertility.
Steiger et al., 2010, J. Biol. Chem. 285(22): 17089--17097 [FBrf0210824]

Non-random genomic integration - an intrinsic property of retrogenes in Drosophila?
Metta and Schlötterer, 2010, BMC Evol. Biol. 10: 114 [FBrf0210914]

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction.
Croset et al., 2010, PLoS Genet. 6(8): e1001064 [FBrf0211681]

Drcd-1 related: a positively selected spermatogenesis retrogene in Drosophila.
Quezada-Díaz et al., 2010, Genetica 138(9-10): 925--937 [FBrf0211952]

Age-dependent chromosomal distribution of male-biased genes in Drosophila.
Zhang et al., 2010, Genome Res. 20(11): 1526--1533 [FBrf0212213]

Molecular evolution of phosphoprotein phosphatases in Drosophila.
Miskei et al., 2011, PLoS ONE 6(7): e22218 [FBrf0214469]

A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes.
Zhang et al., 2011, Bioinformatics 27(13): 1749--1753 [FBrf0216536]

A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits.
Li et al., 2011, BMC Evol. Biol. 11: 337 [FBrf0217002]

Birth, death, and replacement of karyopherins in Drosophila.
Phadnis et al., 2012, Mol. Biol. Evol. 29(5): 1429--1440 [FBrf0218179]

Burst of young retrogenes and independent retrogene formation in mammals.
Pan and Zhang, 2009, PLoS ONE 4(3): e5040 [FBrf0225447]

Personal communication to FlyBase

Helping FlyBase: ADRC-60691.
Mugue, 2007.2.26, Helping FlyBase: ADRC-60691. [FBrf0199143]

Associated Information
Comments

This FlyBase analysis synthesizes the results of 22 publications, of both single-gene and genome-wide scope, that have sought to identify protein coding genes derived by retrotransposition. A total of 685 calls for 420 putative retrotransposed protein coding genes were assessed, of which 142 genes were deemed to represent well supported retrotransposed protein coding genes. These 142 well supported retrogenes were annotated with the SO term 'retrotransposed_protein_coding_gene' (SO:0000569). This term is presented in the 'Gene Model and Products > Sequence Ontology: Class of Gene' section of the gene report. All genes with this annotation can be retrieved using the FlyBase Vocabularies tool (http://flybase.org/cgi-bin/cvreport.pl?rel=is_a& id=SO:0000569 ).

The publications assessed herein are listed in the "Related Publication(s)" section of this FlyBase Reference report. All published calls and subsequent FlyBase analysis are presented in the associated spreadsheet, "FB_retrogenes.2014.8.5.xlsx". The 420 putative retrogenes analyzed, whether or not they were ultimately deemed to represent well supported retrogenes, are listed in the "Data From Reference > Genes" section of this FlyBase Reference report. All 685 putative retrogene assertions from the 22 publications are represented by standardized comments with the key words 'derived' and 'retroposition' in the 'Other Information > Relationship to Other Genes' section of the gene report, attributed to the original publication.

Methods:

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; these publications were identified by searching abstracts containing the terms 'retrogene', 'retroposition' or 'retrotransposition'. This 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.

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 enough 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.

Associated Files
File date: 2014.8.5 ; File size: 52708 ; File format: xlsx ; File name: FB_retrogenes.2014.8.5.xlsx
Other Information
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    Language of Publication
    English
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    Data From Reference
    Genes (420)
    List limited to the first 200 records. Use the HitList export button in the left sidebar to view all records.