Common pattern of evolution of gene expression level and protein sequence in Drosophila
Common pattern of evolution of gene expression level and protein sequence in Drosophila
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DOI：
10.1093/molbev/msh128
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发表时间：
2004-07-01
影响因子：
10.7
通讯作者：
McIntyre, LM
中科院分区：
文献类型：
--
作者：
Nuzhdin, SV;Wayne, ML;McIntyre, LM
物种内的序列差异被用来推断选择对单个基因的作用。将这种方法应用于表达，我们比较了10个杂合果蝇基因型和10个D.黑腹果蝇品系。对D.黑腹果蝇的转录水平低于检测阈值。simulans，这可以通过芯片上的引物和mRNA转录物之间的序列差异或通过这些基因的下调来解释。在两个物种中表达的6，707个基因中，有534个基因的转录水平在物种之间存在显著差异（P < 0.001）。在稳定选择下表达的基因应表现出物种内遗传变异减少和物种间分歧减少。定向选择条件下D. simulans与D. melanogaster，而D. simulans。最后，物种内变异较大但物种间差异较小的基因是平衡选择的候选基因。快速分化的低多态性基因包括那些参与生殖的基因（例如，Mst 3Ba，980; Acps 26 Aa，63 F;和精子特异性动力蛋白）。物种内转录本丰度变化较大的基因包括金属硫蛋白和无毛基因，这两种基因都被假设为由于基因与环境的相互作用而在自然界中分离。此外，我们比较了195个基因的表达差异和DNA替换率。同义替换率与表达差异不相关，而非同义替换率与表达差异显著正相关。我们假设，作为一个相当大的部分非同义分歧已被证明是自适应的，大部分观察到的表达分歧同样是自适应的。
Sequence divergence scaled by variation within species has been used to infer the action of selection upon individual genes. Applying this approach to expression, we compared whole-genome whole-body RNA levels in 10 heterozygous Drosophila simulans genotypes and a pooled sample of 10 D. melanogaster lines using Affymetrix Genechip. For 972 genes expressed in D. melanogaster, the transcript level was below detection threshold in D. simulans, which may be explained either by sequence divergence between the primers on the chip and the mRNA transcripts or by down-regulation of these genes. Out of 6,707 genes that were expressed in both species, transcript level was significantly different between species for 534 genes (at P < 0.001). Genes whose expression is under stabilizing selection should exhibit reduced genetic variation within species and reduced divergence between species. Expression of genes under directional selection in D. simulans should be highly divergent from D. melanogaster, while showing low genetic variation in D. simulans. Finally, the genes with large variation within species but modest divergence between species are candidates for balancing selection. Rapidly diverging, low-polymorphism genes included those involved in reproduction (e.g., Mst 3Ba, 980; Acps 26Aa, 63F; and sperm-specific dynein). Genes with high variation in transcript abundance within species included metallothionein and hairless, both hypothesized to be segregating in nature because of gene-by-environment interactions. Further, we compared expression divergence and DNA substitution rate in 195 genes. Synonymous substitution rate and expression divergences were uncorrelated, whereas there was a significant positive correlation between nonsynonymous substitution rate and expression divergence. We hypothesize that as a substantial fraction of nonsynonymous divergence has been shown to be adaptive, much of the observed expression divergence is likewise adaptive.