Allelic Imbalance in Drosophila Hybrid Heads: Exons, Isoforms, and Evolution
Allelic Imbalance in Drosophila Hybrid Heads: Exons, Isoforms, and Evolution
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DOI：
10.1093/molbev/msr318
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发表时间：
2012-06-01
影响因子：
10.7
通讯作者：
McIntyre, L. M.
中科院分区：
文献类型：
--
作者：
Graze, R. M.;Novelo, L. L.;McIntyre, L. M.
要弄清监管差异是如何导致物种差异和适应的，需要从数百万个遗传差异中识别出功能变异。等位基因不平衡(AI)分析揭示了顺式调节的功能遗传差异，并显示了物种内和种间顺式调节的差异。调控机制通常是高度保守的，但不同物种之间的基因表达差异很大。是什么进化力量解释了独联体监管的广泛差异？利用RNA-SEQ技术对黑腹果蝇和拟果蝇杂交雌性头部的AI进行了评估。通过使用特定于基因型的参考文献，几乎消除了定位偏差。在一种新的贝叶斯模型中，将DNA测序中的等位基因表示作为先验来估计RNA中的AI。顺式调节差异在头部的器官和组织中很常见，分析的基因中有41%显示出显著的人工智能。利用现有的群体基因组数据，研究了人工智能与序列进化模式之间的关系。在30%的顺式调控差异基因中发现了正选择的证据。参与防御的基因、RNAi/RISC复合体基因和性别调控基因在适应性进化的顺式调控差异基因中丰富。对于这些群体中的基因，适应性进化可能在物种之间的调控差异中发挥作用。然而，没有证据表明适应性进化驱动了所观察到的顺式调控差异的大部分。大多数基因表现出与稳定选择和中性进化过程一致的模式。
Unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. Analysis of allelic imbalance (AI) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation within and between species. Regulatory mechanisms are often highly conserved, yet differences between species in gene expression are extensive. What evolutionary forces explain widespread divergence in cis regulation? AI was assessed in Drosophila melanogaster-Drosophila simulans hybrid female heads using RNA-seq technology. Mapping bias was virtually eliminated by using genotype-specific references. Allele representation in DNA sequencing was used as a prior in a novel Bayesian model for the estimation of AI in RNA. Cis regulatory divergence was common in the organs and tissues of the head with 41% of genes analyzed showing significant AI. Using existing population genomic data, the relationship between AI and patterns of sequence evolution was examined. Evidence of positive selection was found in 30% of cis regulatory divergent genes. Genes involved in defense, RNAi/RISC complex genes, and those that are sex regulated are enriched among adaptively evolving cis regulatory divergent genes. For genes in these groups, adaptive evolution may play a role in regulatory divergence between species. However, there is no evidence that adaptive evolution drives most of the cis regulatory divergence that is observed. The majority of genes showed patterns consistent with stabilizing selection and neutral evolutionary processes.