ArticleGenome research2011
Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed, 62 citations in OpenAlex.
- Retrotransposed gene copies persist under relaxed selection in wild Spodoptera frugiperda.Molecular biology and evolution · 2026Article
- Is the extreme within-population genome size variation real in Spodoptera frugiperda?PloS one · 2025Article
- Article
- The roles of gene duplications in the dynamics of evolutionary conflicts.Proceedings. Biological sciences · 2024Review
- Tracing the Origin and Evolutionary Fate of Recent Gene Retrocopies in Natural Populations of the House Mouse.Molecular biology and evolution · 2022Article
- The mutational load in natural populations is significantly affected by high primary rates of retroposition.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization.Frontiers in genetics · 2021Article
- Whole genome-wide chromosome fusion and new gene birth in theCell & bioscience · 2020Article
- Small Segmental Duplications in Drosophila-High Rate of Emergence and Elimination.Genome biology and evolution · 2019Article
- Genes Relocated Between Drosophila Chromosome Arms Evolve Under Relaxed Selective Constraints Relative to Non-Relocated Genes.Journal of molecular evolution · 2018Article
- The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?Genome biology and evolution · 2017Article
- Unveiling the Impact of the Genomic Architecture on the Evolution of Vertebrate microRNAs.Frontiers in genetics · 2017Review
- LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans.Genome research · 2016Article
- Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta).Scientific reports · 2016Article
- Evidence for the fixation of gene duplications by positive selection in Drosophila.Genome research · 2016Article
- LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots.Scientific reports · 2016Article
- The molecular evolution of spiggin nesting glue in sticklebacks.Molecular ecology · 2015Article
- Extensive error in the number of genes inferred from draft genome assemblies.PLoS computational biology · 2014Article
- Relocation facilitates the acquisition of short cis-regulatory regions that drive the expression of retrogenes during spermatogenesis in Drosophila.Molecular biology and evolution · 2014Article
- A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster.Genome research · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Gene duplication via retrotransposition has been shown to be an important mechanism in evolution, affecting gene dosage and allowing for the acquisition of new gene functions. Although fixed retrotransposed genes have been found in a variety of species, very little effort has been made to identify retrogene polymorphisms. Here, we examine 37 Illumina-sequenced North American Drosophila melanogaster inbred lines and present the first ever data set and analysis of polymorphic retrogenes in Drosophila. We show that this type of polymorphism is quite common, with any two gametes in the North American population differing in the presence or absence of six retrogenes, accounting for ~13% of gene copy-number heterozygosity. These retrogenes were identified by a straightforward method that can be applied using any type of DNA sequencing data. We also use a variant of this method to conduct a genome-wide scan for intron presence/absence polymorphisms, and show that any two chromosomes in the population likely differ in the presence of multiple introns. We show that these polymorphisms are all in fact deletions rather than intron gain events present in the reference genome. Finally, by leveraging the known location of the parental genes that give rise to the retrogene polymorphisms, we provide direct evidence that natural selection is responsible for the excess of fixations of retrogenes moving off of the X chromosome in Drosophila. Further efforts to identify retrogene and intron presence/absence polymorphisms will undoubtedly improve our understanding of the evolution of gene copy number and gene structure.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.