Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome.
Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome.
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与洞穴衍生性状相关的基因座集中在墨西哥洞穴鱼基因组的特定区域。
DOI：
10.1101/2024.03.29.587360
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
McGaugh,SuzanneE
中科院分区：
文献类型：
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作者：
Wiese,Jonathan;Richards,Emilie;Kowalko,JohannaE;McGaugh,SuzanneE
现代进化生物学的一个主要目标是将表型进化与其潜在的遗传基础联系起来。墨西哥洞穴鱼（Astyanax mexicanus）是一种由地表生态型和洞穴衍生生态型组成的特征鱼类，非常适合作为研究适应极端环境的遗传机制的模型。在这里，我们将 206 个先前发表的墨西哥 A. mexicanus 洞穴衍生性状的数量性状位点 (QTL) 映射到最新版本的表层鱼类基因组组装 AstMex3。该分析表明，QTL 在基因组中的聚类比预期更多是偶然的，并且这种聚类不能用基因组中基因的分布来解释。为了研究基因组的某些特征是否促进表型进化，我们测试了基因组特征（例如高诱变 CpG 位点）是否是性状进化位点的可靠预测因子，但没有发现任何显着趋势。最后，我们将 QTL 图谱与之前收集的表达和选择数据结合起来，确定了 36 个候选基因的列表，这些基因可能是洞穴表型重复进化的基础，其中包括预计参与光转导的 rgrb。我们发现该基因破坏了所有非杂交洞穴种群的外显子，但在表层鱼类中保留了完整的阅读框。总体而言，我们的结果表明，基因组中特定的“进化热点”可能在推动 Astyanax mexicanus 适应洞穴环境方面发挥重要作用，并证明这个编译的数据集如何有助于我们理解墨西哥洞穴鱼重复进化的遗传基础。
A major goal of modern evolutionary biology is connecting phenotypic evolution with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. This analysis revealed that QTL cluster in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify a list of 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific “evolutionary hotspots” in the genome may play significant roles in driving adaptation to the cave environment in Astyanax mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.