Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura.

TitleEvidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura.
Publication TypeJournal Article
Year of Publication2014
AuthorsFuller, ZL, Haynes, GD, Zhu, D, Batterton, M, Chao, H, Dugan, S, Javaid, M, Jayaseelan, JC, Lee, S, Li, M, Ongeri, F, Qi, S, Han, Y, Doddapaneni, HV, Richards, S, Schaeffer, SW
JournalG3 (Bethesda)
Volume4
Issue12
Pagination2433-49
Date Published2014 Oct 17
ISSN2160-1836
KeywordsAnimals, Chromosomes, Codon, Drosophila, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Recombination, Genetic, Selection, Genetic, Sequence Analysis, DNA
Abstract

There has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. Codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. The efficacy of selection is expected to be reduced in regions of suppressed recombination. Contrary to observations in Drosophila melanogaster, some recent studies have failed to detect a relationship between the recombination rate, intensity of selection acting at synonymous sites, and the magnitude of codon bias as predicted under these standard models. Here, we examined codon bias in 2798 protein coding loci on the third chromosome of D. pseudoobscura using whole-genome sequences of 47 individuals, representing five common third chromosome gene arrangements. Fine-scale recombination maps were constructed using more than 1 million segregating sites. As expected, recombination was demonstrated to be significantly suppressed between chromosome arrangements, allowing for a direct examination of the relationship between recombination, selection, and codon bias. As with other Drosophila species, we observe a strong mutational bias away from the most frequently used codons. We find the rate of synonymous and nonsynonymous polymorphism is variable between different amino acids. However, we do not observe a reduction in codon bias or the strength of selection in regions of suppressed recombination as expected. Instead, we find that the interaction between weak stabilizing selection and mutational bias likely plays a role in shaping the composition of synonymous codons across the third chromosome in D. pseudoobscura.

DOI10.1534/g3.114.014860
Alternate JournalG3 (Bethesda)
PubMed ID25326424
PubMed Central IDPMC4267939
Grant ListR01 GM098478 / GM / NIGMS NIH HHS / United States
T32 GM102057 / GM / NIGMS NIH HHS / United States