快速流动的鲤科鱼类线粒体基因组选择放松的证据。
Evidence for relaxed selection of mitogenome in rapid-flow cyprinids.
机构信息
National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
出版信息
Genes Genomics. 2019 Jul;41(7):863-869. doi: 10.1007/s13258-019-00817-7. Epub 2019 Apr 23.
BACKGROUND
Hypoxia adaptation is developed in many fish species, which helped them to habitat most of water bodies. However, fishes living under high oxygen concentration may lose this feature. Rapid flows provide high level and stable dissolved oxygen, which facilitate organism's oxygen supply and energy production. Previous studies showed that fish species from rapid-flow habitats exhibited lower hypoxia tolerance compared with fish from intermediate- and slow-flow habitats. Mitochondrial genomes code 13 key components in oxidative phosphorylation pathway; these genes may be under relaxed selection in rapid-flow species.
OBJECTIVES
The primary objectives of this study is to investigate the evolutionary patterns of the 13 mitochondrial OXPHOS genes among nine cyprinids from different water bodies and to test the hypotheses that mitochondrial OXPHOS genes may experience relaxed selection in rapid-flow habitats.
METHODS
We classified nine cyprinid fish species into three groups based on their habitats: rapid-flow, intermediate-flow and slow-flow. To detect relaxed selections, we investigated the 13 protein-coding genes with codon evolution programs RELAX; to estimate evolutionary rates among the cyprinids, free-ratio model in Codeml program was applied; Branch-site models were applied to detect positive selection sites. The polymorphisms of homologous sites were evaluated with PROVEAN program and projected to 3D structure prediction of the proteins using SWISS-MODEL.
RESULTS
We found that nine out of the 13 genes are under relaxed selection in rapid-flow species. Furthermore, dN, dS and dN/dS are relatively increased when compared with those of intermediate-flow species. More amino acid polymorphic sites are presented in rapid-flow species than in intermediate- and slow-flow species. Furthermore, rapid-flow species had more deleterious substitutions than other groups. 3D structure prediction of these proteins and projection of the polymorphic sites indicated that these sites were randomly distributed, suggesting relaxed functional constraints of these proteins in rapid-flow species.
CONCLUSION
Our results suggest that mitochondrial genes are under relaxed selection in rapid-flow cyprinids.
背景
许多鱼类物种都具有缺氧适应能力，这使它们能够栖息在大多数水体中。然而，生活在高氧浓度下的鱼类可能会失去这种特征。快速流动的水体会提供高水平且稳定的溶解氧，这有助于满足生物的氧气供应和能量产生。先前的研究表明，来自快速流栖息地的鱼类物种比来自中速和慢速流栖息地的鱼类物种表现出较低的缺氧耐受性。线粒体基因组编码氧化磷酸化途径中的 13 个关键组成部分；这些基因在快速流物种中可能受到松弛选择的影响。
目的
本研究的主要目的是研究来自不同水体的 9 种鲤科鱼类中 13 个线粒体 OXPHOS 基因的进化模式，并检验线粒体 OXPHOS 基因在快速流生境中可能经历松弛选择的假设。
方法
我们根据鱼类的栖息地将 9 种鲤科鱼类分为 3 组：快速流、中速流和慢速流。为了检测松弛选择，我们使用 Codon 进化程序 RELAX 研究了 13 个蛋白质编码基因；为了估计鲤科鱼类之间的进化速率，我们应用了 Codeml 程序中的自由比模型；应用分支位点模型来检测正选择位点。使用 PROVEAN 程序评估同源位点的多态性，并使用 SWISS-MODEL 将其投影到蛋白质的 3D 结构预测中。
结果
我们发现，在快速流物种中，13 个基因中有 9 个处于松弛选择状态。此外，与中速流物种相比，dN、dS 和 dN/dS 相对增加。快速流物种中存在更多的氨基酸多态性位点，比中速和慢速流物种多。此外，快速流物种比其他组具有更多的有害取代。这些蛋白质的 3D 结构预测和多态性位点的投影表明，这些位点是随机分布的，这表明这些蛋白质在快速流物种中的功能约束较为松弛。
结论
我们的研究结果表明，线粒体基因在快速流鲤科鱼类中处于松弛选择状态。
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