Comparative transcriptome analysis of wild and lab populations of Astyanax mexicanus uncovers differential effects of environment and morphotype on gene expression
Comparative transcriptome analysis of wild and lab populations of Astyanax mexicanus uncovers differential effects of environment and morphotype on gene expression
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DOI：
10.1002/jez.b.22933
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发表时间：
2020-02-04
影响因子：
2.2
通讯作者：
Rohner, Nicolas
中科院分区：
文献类型：
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作者：
Krishnan, Jaya;Persons, Jenna L.;Rohner, Nicolas
研究不同基因型如何响应环境变化对于理解适应的遗传基础至关重要。墨西哥四足蜥（Astyanax mexicanus）具有洞穴和地表栖息的形态类型，它们已经适应了完全不同的野外环境，并且现在在实验室条件下成功维持。虽然这使得能够识别各种生理过程背后的遗传适应，但很少有研究直接比较实验室饲养的种群和自然种群之间的形态型。这种比较方法可以帮助剖析环境和形态类型的不同影响，并确定实验室观察到的现象在多大程度上可以推广到现场条件。为此，我们采用转录组学方法在自然栖息地和实验室环境中比较帕雄洞穴鱼和表层鱼类的对应物。我们确定了鱼群之间与新陈代谢和生理学有关的基因表达的关键变化，表明形态类型（表面或洞穴）和环境（自然或实验室）都会改变基因表达。我们发现自然栖息地中洞穴鱼类和表层鱼类之间的基因表达差异远大于实验室环境中形态类型之间的表达差异。然而，实验室饲养的洞穴鱼和水面鱼仍然表现出许多基因表达变化，支持该物种肝脏中基因编码的变化。由此，我们得出结论，受控的实验室环境可能是研究洞穴鱼和表层鱼类代谢和生理差异的遗传基础的理想环境。
Studying how different genotypes respond to environmental variation is essential to understand the genetic basis of adaptation. The Mexican tetra, Astyanax mexicanus, has cave and surface-dwelling morphotypes that have adapted to entirely different environments in the wild, and are now successfully maintained in lab conditions. While this has enabled the identification of genetic adaptations underlying a variety of physiological processes, few studies have directly compared morphotypes between lab-reared and natural populations. Such comparative approaches could help dissect the varying effects of environment and morphotype, and determine the extent to which phenomena observed in the lab are generalizable to conditions in the field. To this end, we take a transcriptomic approach to compare the Pachon cavefish and their surface fish counterparts in their natural habitats and the lab environment. We identify key changes in expression of genes implicated in metabolism and physiology between groups of fish, suggesting that morphotype (surface or cave) and environment (natural or lab) both alter gene expression. We find gene expression differences between cave and surface fish in their natural habitats are much larger than differences in expression between morphotypes in the lab environment. However, lab-raised cave and surface fish still exhibit numerous gene expression changes, supporting genetically encoded changes in livers of this species. From this, we conclude that a controlled laboratory environment may serve as an ideal setting to study the genetic underpinnings of metabolic and physiological differences between the cavefish and surface fish.