Codon usage bias and effective population sizes on the X chromosome versus the autosomes in Drosophila melanogaster.
Codon usage bias and effective population sizes on the X chromosome versus the autosomes in Drosophila melanogaster.
复制标题
X染色体上的密码子使用偏差和有效的人口大小与果蝇果蝇中的常染色体相比。
DOI：
10.1093/molbev/mss222
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发表时间：
2013-04
影响因子：
10.7
通讯作者：
Haddrill PR
中科院分区：
文献类型：
--
作者：
Campos JL;Zeng K;Parker DJ;Charlesworth B;Haddrill PR
果蝇中X连锁基因的密码子使用偏好（CUB）高于常染色体基因。一个可能的解释是，与常染色体相比，X染色体上基因的有效重组率更高，降低了它们对Hill-Robertson效应的敏感性，从而增强了密码子选择的效力。对D.用黑腹鱼来检验这一假设。与预期相反，发现校正有效重组率后，CUB在X染色体上仍高于常染色体。与此相反，从卢旺达人口的多态性数据的分析表明，平均核苷酸位点多样性在4倍的简并位点上的X基因是约四分之三的常染色体值校正后的有效重组率，与近似平等校正前相比。此外，这些数据表明，X染色体上对首选同义变体与非首选同义变体的选择比常染色体上的选择更强，这解释了X染色体上基因的较高CUB。这种选择强度的差异似乎并不反映影响密码子使用的突变显性效应、X和常染色体之间基因表达水平的差异或突变偏倚的差异。因此，其原因仍然无法解释。与常染色体相比，X染色体上的CUB上的较强选择导致同义位点分歧率较低;对于基于McDonald-Kreitman检验的方法，这将导致X比A更强的正选择固定的非同义突变比例的估计的向上偏倚。
Codon usage bias (CUB) in Drosophila is higher for X-linked genes than for autosomal genes. One possible explanation is that the higher effective recombination rate for genes on the X chromosome compared with the autosomes reduces their susceptibility to Hill–Robertson effects, and thus enhances the efficacy of selection on codon usage. The genome sequence of D. melanogaster was used to test this hypothesis. Contrary to expectation, it was found that, after correcting for the effective recombination rate, CUB remained higher on the X than on the autosomes. In contrast, an analysis of polymorphism data from a Rwandan population showed that mean nucleotide site diversity at 4-fold degenerate sites for genes on the X is approximately three-quarters of the autosomal value after correcting for the effective recombination rate, compared with approximate equality before correction. In addition, these data show that selection for preferred versus unpreferred synonymous variants is stronger on the X than the autosomes, which accounts for the higher CUB of genes on the X chromosome. This difference in the strength of selection does not appear to reflect the effects of dominance of mutations affecting codon usage, differences in gene expression levels between X and autosomes, or differences in mutational bias. Its cause therefore remains unexplained. The stronger selection on CUB on the X chromosome leads to a lower rate of synonymous site divergence compared with the autosomes; this will cause a stronger upward bias for X than A in estimates of the proportion of nonsynonymous mutations fixed by positive selection, for methods based on the McDonald–Kreitman test.
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影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
DOI：
10.1073/pnas.96.8.4482
发表时间：
1999-04-13
影响因子：
11.1
作者：
Duret, L;Mouchiroud, D
通讯作者：
Mouchiroud, D
影响因子：
1.5
作者：
Charlesworth, B
通讯作者：
Charlesworth, B
影响因子：
64.8
作者：
Fay, JC;Wyckoff, GJ;Wu, CI
通讯作者：
Wu, CI
影响因子：
3.3
作者：
Hutter, Stephan;Li, Haipeng;Stephan, Wolfgang
通讯作者：
Stephan, Wolfgang