Movement of transposable elements contributes to cichlid diversity
Movement of transposable elements contributes to cichlid diversity
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DOI：
10.1111/mec.15685
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发表时间：
2020-11-13
影响因子：
4.9
通讯作者：
Kocher, Thomas D.
中科院分区：
文献类型：
--
作者：
Carleton, Karen L.;Conte, Matthew A.;Kocher, Thomas D.
非洲丽鱼是研究物种形成机制的主要模式。尽管开发了广泛的基因组资源，但很难确定哪些遗传变异来源是造成慈鲷表型变异的原因。它们最多变的表型之一是视觉敏感性，在脊椎动物中具有最大的光谱变化。这些变化主要来自七个视锥细胞视蛋白基因的差异表达。通过绘制马拉维湖慈鲷属间杂交的表达数量性状基因座（eQTL），我们以前确定了四个致病的遗传变异，对应于关键转录因子或视蛋白基因启动子中的插入缺失。在这项全面的研究中，我们表明，这些插入缺失是与马拉维鸡群中视蛋白表达变化相关的转座因子（TE）运动的结果。在跟踪这些特定的插入缺失的进化历史，我们发现他们是马拉维湖特有的，这表明这些TE最近是活跃的，并在马拉维慈鲷谱系内分离。然而，一个独立的插入缺失出现在一个类似的基因组位置在一个位点以外的马拉维羊群。TE运动中的会聚表明这些位点为TE插入和随后的缺失做好了准备。TE迁移率的增加可能与种间杂交有关，这种杂交破坏了TE抑制的机制。这可能提供了慈鲷杂交和加速监管变化之间的联系。总的来说，我们的研究表明，TE可能是关键监管变化的重要驱动因素，促进了非洲慈鲷的快速表型变化和可能的物种形成。
African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids.