Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes.
Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes.
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DOI：
10.1111/mec.16700
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发表时间：
2022-11
影响因子：
4.9
通讯作者：
Peng, Zuogang
中科院分区：
文献类型：
--
作者：
Zhao, Qingyuan;Shao, Feng;Li, Yanping;Yi, Soojin, V;Peng, Zuogang
所有生活在世界各地洞穴中的洞穴鱼都表现出相似的表型特征，包括失去眼睛的特征。为了了解这种表型趋同是否具有相似的基因组碱基，我们通过比较三对洞穴鱼及其表层亲缘鱼的全基因组序列，研究了洞穴鱼表型的全基因组进化特征。值得注意的是，我们对中国洞穴鱼（Triplophysa rosa）的全基因组进行了测序和组装。我们的比较分析揭示了洞穴鱼基因组进化的几个共同特征。洞穴鱼的突变率比它们的表层鱼类亲戚要低。相反，与表层鱼类相比，洞穴鱼类的非同义与同义替换比率（ω）显著升高，这与净化选择的放松一致。此外，洞穴鱼基因组的突变负荷增加，包括改变蛋白质疏水性谱的突变，这被认为是有害的。然而，有趣的是，我们发现不同穴居鱼谱系的正选择基因没有重叠，这表明穴居鱼的表型趋同不是由同一组基因的正选择引起的。对先前确定的与洞穴表型相关的候选基因的分析支持了这一结论。所有洞穴鱼基因组中属于脂质代谢功能本体的基因都处于宽松的纯化选择状态，这可能与洞穴鱼的营养贫乏栖息地有关。我们的工作揭示了洞穴鱼基因组进化的先前未表征的模式，并提供了洞穴相关表型性状进化的比较见解。
All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome‐wide evolutionary signatures of cavefish phenotypes by comparing whole‐genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole‐genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient‐poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave‐associated phenotypic traits.
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