Variable strength of translational selection among 12 Drosophila species

Genetics
Andreas Heger, Chris P Ponting

Abstract

Codon usage bias in Drosophila melanogaster genes has been attributed to negative selection of those codons whose cellular tRNA abundance restricts rates of mRNA translation. Previous studies, which involved limited numbers of genes, can now be compared against analyses of the entire gene complements of 12 Drosophila species whose genome sequences have become available. Using large numbers (6138) of orthologs represented in all 12 species, we establish that the codon preferences of more closely related species are better correlated. Differences between codon usage biases are attributed, in part, to changes in mutational biases. These biases are apparent from the strong correlation (r = 0.92, P < 0.001) among these genomes' intronic G + C contents and exonic G + C contents at degenerate third codon positions. To perform a cross-species comparison of selection on codon usage, while accounting for changes in mutational biases, we calibrated each genome in turn using the codon usage bias indices of highly expressed ribosomal protein genes. The strength of translational selection was predicted to have varied between species largely according to their phylogeny, with the D. melanogaster group species exhibiting the strongest degree o...Continue Reading

References

Jul 22, 1991·FEBS Letters·C G Kurland
Jun 20, 1991·Nature·P H Harvey, A Purvis
May 1, 1989·Journal of Molecular Evolution·P M Sharp, W H Li
Jan 1, 1986·Journal of Molecular Evolution·P M Sharp, W H Li
Jul 22, 1997·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey R Powell, Etsuko N Moriyama
Oct 29, 1997·Journal of Molecular Evolution·Etsuko N Moriyama, Jeffrey R Powell
Jun 6, 1998·Journal of Molecular Evolution·R M Kliman, A Eyre-Walker
Feb 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·Dmitri A Petrov, D L Hartl
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·Laurent Duret, D Mouchiroud
Mar 25, 2000·Science·M D AdamsJ C Venter
Nov 9, 2000·Molecular Biology and Evolution·F Rodríguez-TrellesF J Ayala
Jun 23, 2001·Molecular Biology and Evolution·David J Begun
Oct 9, 2002·Proceedings of the National Academy of Sciences of the United States of America·Andrea J Betancourt, Daven C Presgraves
Nov 16, 2002·Current Opinion in Genetics & Development·Laurent Duret
Sep 2, 2003·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Nov 5, 2003·Bioinformatics·A CarboneF Képès
Jan 24, 2004·Current Biology : CB·Xulio MasideBrian Charlesworth
Mar 11, 2004·Journal of Molecular Evolution·Jeffrey R PowellAdalgisa Caccone
Sep 17, 2004·Molecular Biology and Evolution·Aaron E HirshDennis P Wall
Feb 17, 2005·BMC Bioinformatics·Guy St C Slater, E Birney
Oct 21, 2005·Nature·Peter Andolfatto
Dec 31, 2005·Nucleic Acids Research·Gary Grumbling, Victor Strelets
Dec 31, 2005·Nucleic Acids Research·E BirneyT J P Hubbard
Jan 13, 2006·Journal of Evolutionary Biology·N Bierne, A Eyre-Walker
May 2, 2006·Molecular Phylogenetics and Evolution·Yuji Inagaki, Andrew J Roger
Oct 3, 2006·PLoS Computational Biology·Leo Goodstadt, Chris P Ponting
Nov 9, 2007·Genome Research·Andreas Heger, Chris P Ponting
Nov 13, 2007·Nature·Drosophila 12 Genomes ConsortiumIain MacCallum
Oct 1, 1998·Evolution; International Journal of Organic Evolution·José Alexandre Felizola Diniz-FilhoLuis Mauricio Bini

Citations

Nov 20, 2012·Genome Biology and Evolution·Yu-Ping PohDavid J Begun
Apr 9, 2009·Molecular Biology and Evolution·Nadia D SinghCharles F Aquadro
Dec 17, 2009·Molecular Biology and Evolution·J Roman ArguelloManyuan Long
Aug 19, 2011·Biology Letters·Sophie Marion de ProcéBrian Charlesworth
Jun 28, 2008·Genome Research·Alisha K HollowayKatherine S Pollard
Nov 9, 2007·Genome Research·Andreas Heger, Chris P Ponting
Aug 15, 2012·Biological Reviews of the Cambridge Philosophical Society·Susanta K Behura, David W Severson
May 14, 2008·BMC Evolutionary Biology·Camila J MazzoniAlexandre A Peixoto
Apr 1, 2014·Nucleic Acids Research·Hervé RouaultVincent Hakim
Apr 30, 2014·Annual Review of Genomics and Human Genetics·Wilfried Haerty, Chris P Ponting
Sep 22, 2010·Molecular Biology and Evolution·Suo QiuDeborah Charlesworth
Sep 17, 2009·Molecular Ecology·K G McCrackenM D Sorenson
Jan 28, 2009·Journal of Evolutionary Biology·N Petit, A Barbadilla
Apr 14, 2011·Molecular Systems Biology·Hila Gingold, Yitzhak Pilpel
Mar 17, 2009·Current Biology : CB·Andrea J BetancourtBrian Charlesworth
Jun 19, 2012·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Olaf RodriguezSusanta K Behura
Aug 3, 2016·Journal of Molecular Evolution·Jae Young Choi, Charles F Aquadro
Oct 10, 2009·Medicine, Conflict, and Survival·Martin Desvaux
Nov 18, 2016·F1000Research·Elena M Bennett, Rebecca Chaplin-Kramer
May 3, 2018·Genetics·Patrick M O'Grady, Rob DeSalle
Mar 6, 2015·G3 : Genes - Genomes - Genetics·Wilson LeungSarah C R Elgin

Related Concepts

Metazoa
G+C Composition
Sense Codon
DNA, Double-Stranded
Drosophila
Drosophila melanogaster
Introns
Phylogeny
Ribosomal Proteins
Selection, Genetic

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