Analysis of a Shift in Codon Usage in Drosophila

Jeffrey R. Powell, Erminia Sezzi, Etsuko N. Moriyama, Jennifer M. Gleason, Adalgisa Caccone

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

In order to gain further insight into a shift in codon usage first observed in Drosophila willistoni we have analyzed seven genes in six species in the lineage leading to D. willistoni. This lineage contains the willistoni and saltans species groups. Sequences were obtained from GenBank or newly sequenced for this study. All species studied showed significant difference in codon usage compared to D. melanogaster for about one third of all amino acids. Within the willistoni/saltans lineage, codon usage is homogeneous, indicating that the shift in codon usage occurred prior to the diversification of extant species in this lineage which we estimate to date to about 20 million years ago. Thus the shift is old and has been stable. We also examined introns from these genes and the G/C composition at four-fold degenerate sites in an effort to detect a change in mutation bias. There is little or no evidence for a difference in mutation bias compared to D. melanogaster. We also considered whether relaxed selection (possibly due to reduced population sizes) or reduced recombination (due to numerous naturally occurring inversions) could account for the shift and concluded these factors alone are insufficient to explain the patterns observed. A change in the relative abundance of isoaccepting tRNAs is one of the few explanations that can account for the observations. Particularly intriguing is the fact that the greatest changes in codon usage have occurred for amino acids with two-fold C/T ending codons for which it is known that posttranscriptional modification occurs in tRNAs from a G in the wobble position to Queuosine that changes optimal binding from C to a slight preference for U. However, we do not argue that this shift was adaptive in nature, rather it may be an example of a "frozen accident.".

Original languageEnglish (US)
Pages (from-to)S214-S225
JournalJournal of Molecular Evolution
Volume57
Issue numberSUPPL. 1
DOIs
StatePublished - Dec 29 2003

Fingerprint

Transfer RNA
codons
Codon
Drosophila
Nucleoside Q
Genes
Amino Acids
Introns
mutation
Accidents
Melanogaster
amino acid
fold
gene
Chemical analysis
recombination
accident
population size
relative abundance
Mutation

Keywords

  • Codon usage bias
  • Drosophila saltans
  • Drosophila willistoni
  • tRNA

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Powell, J. R., Sezzi, E., Moriyama, E. N., Gleason, J. M., & Caccone, A. (2003). Analysis of a Shift in Codon Usage in Drosophila. Journal of Molecular Evolution, 57(SUPPL. 1), S214-S225. https://doi.org/10.1007/s00239-003-0030-3

Analysis of a Shift in Codon Usage in Drosophila. / Powell, Jeffrey R.; Sezzi, Erminia; Moriyama, Etsuko N.; Gleason, Jennifer M.; Caccone, Adalgisa.

In: Journal of Molecular Evolution, Vol. 57, No. SUPPL. 1, 29.12.2003, p. S214-S225.

Research output: Contribution to journalArticle

Powell, JR, Sezzi, E, Moriyama, EN, Gleason, JM & Caccone, A 2003, 'Analysis of a Shift in Codon Usage in Drosophila', Journal of Molecular Evolution, vol. 57, no. SUPPL. 1, pp. S214-S225. https://doi.org/10.1007/s00239-003-0030-3
Powell, Jeffrey R. ; Sezzi, Erminia ; Moriyama, Etsuko N. ; Gleason, Jennifer M. ; Caccone, Adalgisa. / Analysis of a Shift in Codon Usage in Drosophila. In: Journal of Molecular Evolution. 2003 ; Vol. 57, No. SUPPL. 1. pp. S214-S225.
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