CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Genes (Basel). 2020 Jan 22;11(2):123. doi: 10.3390/genes11020123.
Genetic adaptation to extremes is a fascinating topic. Nevertheless, few studies have explored the genetic adaptation of closely related species respectively inhabiting distinct extremes. With deep transcriptome sequencing, we attempt to detect the genetic architectures of tadpoles of five closely related toad species adapted to the Tibetan Plateau, middle-altitude mountains and karst caves. Molecular evolution analyses indicated that not only the number of fast evolving genes (FEGs), but also the functioning coverage of FEGs, increased with elevation. Enrichment analyses correspondingly revealed that the highland species had most of the FEGs involved in high-elevation adaptation, for example, amino acid substitutions of XRCC6 in its binding domains might improve the capacity of DNA repair of the toad. Yet, few FEGs and positively selected genes (PSGs) involved in high-elevation adaptation were identified in the cave species, and none of which potentially contributed to cave adaptation. Accordingly, it is speculated that in the closely related toad tadpoles, genetic selection pressures increased with elevation, and cave adaptation was most likely derived from other factors (e.g., gene loss, pseudogenization or deletion), which could not be detected by our analyses. The findings supply a foundation for understanding the genetic adaptations of amphibians inhabiting extremes.
遗传适应极端环境是一个引人入胜的话题。然而，很少有研究分别探讨分别栖息在截然不同的极端环境中的密切相关物种的遗传适应。通过深度转录组测序，我们试图检测适应青藏高原、中海拔山脉和喀斯特洞穴的 5 种密切相关蟾蜍的蝌蚪的遗传结构。分子进化分析表明，不仅快速进化基因（FEG）的数量增加，而且 FEG 的功能覆盖度也随着海拔的升高而增加。相应的富集分析表明，高原物种拥有大多数与高海拔适应相关的 FEG，例如 XRCC6 结合域中的氨基酸替换可能会提高蟾蜍的 DNA 修复能力。然而，在洞穴物种中只鉴定到少数与高海拔适应相关的 FEG 和正选择基因（PSG），而且它们都不能促进洞穴适应。因此，可以推测在密切相关的蟾蜍蝌蚪中，遗传选择压力随着海拔的升高而增加，而洞穴适应很可能来自于其他因素（例如，基因丢失、假基因化或缺失），这些因素无法通过我们的分析检测到。这些发现为理解栖息在极端环境中的两栖动物的遗传适应提供了基础。
