GC-biased segregation of noncoding polymorphisms in Drosophila

Genetics
Nicolas GaltierNicolas Bierne

Abstract

The study of base composition evolution in Drosophila has been achieved mostly through the analysis of coding sequences. Third codon position GC content, however, is influenced by both neutral forces (e.g., mutation bias) and natural selection for codon usage optimization. In this article, large data sets of noncoding DNA sequence polymorphism in D. melanogaster and D. simulans were gathered from public databases to try to disentangle these two factors-noncoding sequences are not affected by selection for codon usage. Allele frequency analyses revealed an asymmetric pattern of AT vs. GC noncoding polymorphisms: AT --> GC mutations are less numerous, and tend to segregate at a higher frequency, than GC --> AT ones, especially at GC-rich loci. This is indicative of nonstationary evolution of base composition and/or of GC-biased allele transmission. Fitting population genetics models to the allele frequency spectra confirmed this result and favored the hypothesis of a biased transmission. These results, together with previous reports, suggest that GC-biased gene conversion has influenced base composition evolution in Drosophila and explain the correlation between intron and exon GC content.

References

Oct 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·T Nagylaki
Jun 6, 1998·Journal of Molecular Evolution·Richard M Kliman, Adam Eyre-Walker
Sep 4, 1999·Journal of Molecular Evolution·Richard M Kliman
Feb 2, 2000·Journal of Molecular Evolution·F Rodríguez-TrellesF J Ayala
Apr 26, 2001·Proceedings of the National Academy of Sciences of the United States of America·G MaraisLaurent Duret
May 24, 2001·Molecular Biology and Evolution·N G Smith, Adam Eyre-Walker
Jul 4, 2001·Nature Reviews. Genetics·Adam Eyre-Walker, L D Hurst
Jan 28, 2003·Trends in Genetics : TIG·Nicolas Galtier
Jun 13, 2003·Trends in Genetics : TIG·Gabriel A B Marais
Jul 23, 2003·Genetical Research·Gabriel A B MaraisLaurent Duret
Feb 14, 2004·Molecular Biology and Evolution·Julien Meunier, Laurent Duret
Apr 16, 2004·Molecular Biology and Evolution·Grzegorz KudlaLeszek Lipinski
Nov 17, 2004·Genetics·Carolina BartoloméBrian Charlesworth
Dec 21, 2004·Nucleic Acids Research·Eric BazinNicolas Galtier

Citations

Mar 25, 2011·Genetics Research·Brian Charlesworth
Nov 20, 2012·Genome Biology and Evolution·Yu-Ping PohDavid J Begun
Apr 9, 2009·Molecular Biology and Evolution·Nadia D SinghCharles F Aquadro
May 29, 2008·Biology Letters·Penelope R Haddrill, Brian Charlesworth
Aug 19, 2011·Biology Letters·Sophie Marion de ProcéBrian Charlesworth
Jul 28, 2009·Annual Review of Genomics and Human Genetics·Laurent Duret, Nicolas Galtier
Oct 17, 2012·PLoS Genetics·Josep M ComeronSamuel Bailin
Jun 12, 2013·PLoS Genetics·Ephraim Kenigsberg, Amos Tanay
Oct 16, 2008·Genetics·Michael M Desai, Joshua B Plotkin
Mar 11, 2010·Genetics·Claudio CasolaMatthew W Hahn
Sep 29, 2011·Genetics·Toni I GossmannAdam Eyre-Walker
Jul 6, 2014·PLoS Genetics·Sasha A LangleyCharles H Langley
Nov 12, 2013·Molecular Biology and Evolution·Matthew C RobinsonNadia D Singh
May 31, 2006·PLoS Genetics·James H Degnan, Noah A Rosenberg
Apr 26, 2007·Journal of Molecular Evolution·Doris Bachtrog
Feb 22, 2008·Journal of Molecular Evolution·Ana LlopartRichard M Kliman
Dec 31, 2009·Journal of Molecular Evolution·Kai Zeng, Brian Charlesworth
Jun 2, 2007·DNA Sequence : the Journal of DNA Sequencing and Mapping·Rong ChenGuang B Liu
Sep 6, 2012·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Sheng Sun, Joseph Heitman
Aug 3, 2016·Journal of Molecular Evolution·Jae Young Choi, Charles F Aquadro
May 18, 2020·Genetics·Tuomas Hämälä, Peter Tiffin
Mar 30, 2011·Molecular Biology and Evolution·Juan S EscobarNicolas Galtier
Dec 14, 2011·Molecular Biology and Evolution·Raquel Assis, Alexey S Kondrashov
May 26, 2012·Genome Biology and Evolution·Eugénie PessiaGabriel A B Marais
Aug 27, 2015·G3 : Genes - Genomes - Genetics·Antonio Marco

Related Concepts

Genome Mapping
Drosophila melanogaster
Phylogeny
Genetic Polymorphism
Selection, Genetic
Base Pairing
Chromosome Segregation
Untranslated Regions
GC Rich Sequence

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Lipidomics & Rhinovirus Infection

Lipidomics can be used to examine the lipid species involved with pathogenic conditions, such as viral associated inflammation. Discovered the latest research on Lipidomics & Rhinovirus Infection.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Torsion Dystonia

Torsion dystonia is a movement disorder characterized by loss of control of voluntary movements appearing as sustained muscle contractions and/or abnormal postures. Here is the latest research.

Archaeal RNA Polymerase

Archaeal RNA polymerases are most similar to eukaryotic RNA polymerase II but require the support of only two archaeal general transcription factors, TBP (TATA-box binding protein) and TFB (archaeal homologue of the eukaryotic general transcription factor TFIIB) to initiate basal transcription. Here is the latest research on archaeal RNA polymerases.

Alzheimer's Disease: MS4A

Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.

Central Pontine Myelinolysis

Central Pontine Myelinolysis is a neurologic disorder caused most frequently by rapid correction of hyponatremia and is characterized by demyelination that affects the central portion of the base of the pons. Here is the latest research on this disease.