Codon usage in twelve species of Drosophila

Abstract

Background: Codon usage bias (CUB), the uneven use of synonymous codons, is a ubiquitous observation in virtually all organisms examined. The pattern of codon usage is generally similar among closely related species, but differs significantly among distantly related organisms, e.g., bacteria, yeast, and Drosophila. Several explanations for CUB have been offered and some have been supported by observations and experiments, although a thorough understanding of the evolutionary forces (random drift, mutation bias, and selection) and their relative importance remains to be determined. The recently available complete genome DNA sequences of twelve phylogenetically defined species of Drosophila offer a hitherto unprecedented opportunity to examine these problems. We report here the patterns of codon usage in the twelve species and offer insights on possible evolutionary forces involved.

Evolution of genes and genomes on the Drosophila phylogeny

“…Codon bias is thought to enhance the efficiency and/or accuracy of translation [99][100][101] and seems to be maintained by mutation-selection-drift balance [101][102][103][104] . Across the 12 Drosophila genomes, there is more codon bias in the Sophophora subgenus than in the Drosophila subgenus, and a previously noted [105][106][107][108][109] striking reduction in codon bias in D. willistoni 110,111 (Fig. 5).…”

“…5). Mutation alone is not sufficient to explain codonusage bias in D. willistoni, which is suggestive of a lineage-specific shift in codon preferences 111,112 . We found evidence for a lineagespecific genomic reduction in codon bias in D. melanogaster (Fig.…”

Analysis of synonymous codon usage patterns in duck hepatitis A virus: a comparison on the roles of mutual pressure and natural selection

“…We simply USE the codon usage table for Escherichia coli as the reference to compute the CAI index for HAV. Because ENC can be driven by both mutation and selection [20], it might not be a robust index to show the relative contribution of mutation and selection on structuring codon usage patterns. Moreover, the codon usage bias of base composition of the ORFs of a species with A/T biased genomes will behave differentially than those species with G/C biased genomes, as such, ENC-GC3s plot might be potentially misleading.…”

“…Moreover, the codon usage bias of base composition of the ORFs of a species with A/T biased genomes will behave differentially than those species with G/C biased genomes, as such, ENC-GC3s plot might be potentially misleading. In contrast, CAI is suggested as the most powerful index for showing the influence of natural selection on codon usage patterns [4,15,20]. If CAI value is high, then codon usage bias is extremely high and the influence of natural selection is prevailing.…”

“…If CAI value is high, then codon usage bias is extremely high and the influence of natural selection is prevailing. Thus, some previous studies [20] suggested to utilize the correlation between CAI and ENC values to show the relative influence of mutation and selection. If selection is more important, the correlation (r) between the two quantities should be very high (r ?…”