De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes.
De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes.
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DOI：
10.1371/journal.pone.0053553
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Rétaux S
中科院分区：
文献类型：
--
作者：
Hinaux H;Poulain J;Da Silva C;Noirot C;Jeffery WR;Casane D;Rétaux S
Astyanax mexicanus是一种具有水面生活（表层鱼）和洞穴适应（洞穴鱼）形态的硬骨鱼，是进化发育生物学（evodevo）中一个重要的模式系统。Astyanax洞穴鱼在许多特征上与水面鱼类不同，包括非视觉感觉系统的增强，眼睛和色素的丧失。由于缺乏基因组和转录组学数据，这些差异的遗传基础尚未完全了解。我们在这里使用Sanger方法对来自Pachón洞穴的表层鱼类种群和洞穴鱼类种群的胚胎和幼虫阶段进行从头转录组测序。这项工作代表了Astyanax研究界的第一个大规模序列和克隆资源。对这些序列的分析表明，与表层鱼类相比，洞穴鱼的多态性水平较低，证实了之前对少数基因的研究。已知洞穴鱼中有很大比例的突变基因在斑马鱼的视觉系统中表达。洞穴鱼的眼睛基因突变如此之多，可以解释为在没有光线的进化过程中对视觉的放松选择。基于这些序列差异，我们列出了11个可能在洞穴鱼视觉系统退化中起作用的基因。
Astyanax mexicanus, a teleost species with surface dwelling (surface fish) and cave adapted (cavefish) morphs, is an important model system in evolutionary developmental biology (evodevo). Astyanax cavefish differ from surface fish in numerous traits, including the enhancement of non-visual sensory systems, and the loss of eyes and pigmentation. The genetic bases for these differences are not fully understood as genomic and transcriptomic data are lacking. We here present de novo transcriptome sequencing of embryonic and larval stages of a surface fish population and a cavefish population originating from the Pachón cave using the Sanger method. This effort represents the first large scale sequence and clone resource for the Astyanax research community. The analysis of these sequences show low levels of polymorphism in cavefish compared to surface fish, confirming previous studies on a small number of genes. A high proportion of the genes mutated in cavefish are known to be expressed in the zebrafish visual system. Such a high number of mutations in cavefish putative eye genes may be explained by relaxed selection for vision during the evolution in the absence of light. Based on these sequence differences, we provide a list of 11 genes that are potential candidates for having a role in cavefish visual system degeneration.
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影响因子：
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作者：
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通讯作者：
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DOI：
10.1016/j.cbpa.2010.03.030
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