Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes.
Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes.
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DOI：
10.1093/gbe/evv192
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发表时间：
2015-10-09
影响因子：
3.3
通讯作者：
He S
中科院分区：
文献类型：
--
作者：
Wang Y;Yang L;Zhou K;Zhang Y;Song Z;He S
高原鳅属鱼类是青藏高原鱼类区系的主要组成部分，对高海拔环境具有很好的适应性。高原鳅属鱼类在高原环境中具有重要意义，但其适应高原环境的遗传机制仍知之甚少。在这项研究中，我们产生的转录组序列的三个高原鳅鱼类，即高原鳅siluroides，高原鳅scleroptera和高原鳅dalaica，并使用这些和以前可用的转录组和基因组序列生活在低海拔地区的鱼类，以确定潜在的遗传机制高原鳅鱼类的高海拔适应性。洞穴鱼类2，269个正向同源基因的分析（Astyanax mexicanus），斑马鱼（Danio rerio），大型泥鳅（Paramisgurnus dabryanus）和高原鳅属鱼类的基因组序列分析表明，高原鳅属鱼类的每个末端分支的非同义替换与同义替换的比率显著高于低海拔鱼类的分支，这为高原鳅属的全基因组快速进化提供了一致的证据。与大型泥鳅相比，高原鳅属鱼类中与能量代谢和低氧反应相关的许多GO（基因本体论）类别表现出加速进化。高原鳅属鱼类中表现出正选择和快速进化迹象的基因也在能量代谢和低氧反应类别中显着富集。我们的分析确定了广泛的高原鳅属特异性非同义突变的快速进化的基因和积极选择的基因。此外，我们发现高原鳅属鱼类的HIF-1A和HIF-2B基因存在显著的正选择证据，并发现高原鳅属特有的HIF-1A和HIF-2B基因的非同义突变与功能变化相关。总体而言，我们的研究为青藏高原高海拔环境中鱼类的适应和进化提供了新的见解，并补充了先前关于哺乳动物和鸟类适应高海拔的研究结果。
Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides, Triplophysa scleroptera, and Triplophysa dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
12.3
作者：
Cai Q;Qian X;Lang Y;Luo Y;Xu J;Pan S;Hui Y;Gou C;Cai Y;Hao M;Zhao J;Wang S;Wang Z;Zhang X;He R;Liu J;Luo L;Li Y;Wang J
通讯作者：
Wang J
DOI：
10.1073/pnas.0701705104
发表时间：
2007-05-01
影响因子：
11.1
作者：
Bakewell, Margaret A.;Shi, Peng;Zhang, Jianzhi
通讯作者：
Zhang, Jianzhi
DOI：
10.1073/pnas.0911239106
发表时间：
2009-12-08
影响因子：
11.1
作者：
Goodman, Morris;Sterner, Kirstin N.;Wildman, Derek E.
通讯作者：
Wildman, Derek E.
DOI：
10.1073/pnas.1002443107
发表时间：
2010-06-22
影响因子：
11.1
作者：
Beall, Cynthia M.;Cavalleri, Gianpiero L.;Zheng, Yong Tang
通讯作者：
Zheng, Yong Tang