Marais Gabriel, Domazet-Loso Tomislav, Tautz Diethard, Charlesworth Brian
Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, EH9 3JT, Scotland, UK.
J Mol Evol. 2004 Dec;59(6):771-9. doi: 10.1007/s00239-004-2671-2.
Recent work has shown that Drosophila melanogaster genes with fast-evolving nonsynonymous sites have lower codon usage bias. This pattern has been attributed to interference between positive selection at nonsynonymous sites and weak selection on codon usage. Here we have looked for this correlation in a much larger and less biased dataset, comprising 630 gene pairs from D. melanogaster and D. yakuba. We confirmed that there is a negative correlation between the rate of nonsynonymous substitutions (d(N)) and codon bias in D. melanogaster. We then tested the interference hypothesis and other alternative explanations, including one involving gene expression. We found that d(N) indeed correlates with the level of gene expression. Given that gene expression is a strong determinant of codon bias, the relationship between d(N) and codon bias might be a by-product of gene expression. However, our tests show that none of the hypotheses we consider seem to explain the data fully.
最近的研究表明，黑腹果蝇中具有快速进化的非同义位点的基因，其密码子使用偏好较低。这种模式被归因于非同义位点的正选择与密码子使用上的弱选择之间的干扰。在这里，我们在一个更大且偏差较小的数据集中寻找这种相关性，该数据集包含来自黑腹果蝇和雅库布果蝇的630对基因。我们证实，黑腹果蝇中非同义替换率（d(N)）与密码子偏好之间存在负相关。然后，我们检验了干扰假说以及其他替代解释，包括一种涉及基因表达的解释。我们发现d(N)确实与基因表达水平相关。鉴于基因表达是密码子偏好的一个重要决定因素，d(N)与密码子偏好之间的关系可能是基因表达的一个副产品。然而，我们的检验表明，我们所考虑的假说似乎都不能完全解释这些数据。
