Data from: Comparative transcriptomic analysis revealed adaptation mechanism of Phrynocephalus erythrurus, the highest altitude lizard living in the Qinghai-Tibet Plateau

Background: Organisms living at high altitudes must overcome three major environmental challenges: hypoxia, cold, and intense UV radiation. The molecular mechanisms that enable these challenges to be overcome have mainly been studied in endothermic organisms; relatively little attention has been paid to poikilothermic species. Here, we present deep transcriptome sequencing in two closely related lizards, the high altitude-dwelling Phrynocephalus erythrurus and the lowland-dwelling P. putjatia, to identify candidate genes under positive selection and to explore the convergent evolutionary adaptation of poikilothermic animals to high altitude life. Results: More than 70 million sequence reads were generated for each species via Illumina sequencing. De novo assembly produced 56,845 and 63,140 transcripts for P. erythrurus and P. putjatia, respectively. P. erythrurus had higher Ka/Ks ratios than P. putjatia, implying an accelerated evolutionary rate in the high altitude lizard lineage. 206 gene ontology (GO) categories with accelerated evolutionary rates and 43 candidate positively selected genes were detected along the P. erythrurus lineage. Some of these GO categories have functions associated with responses to hypoxia, energy metabolism and responses to UV damage. We also found that the high-altitude ranid frog R. kukunoris had higher Ka/Ks ratios than the closely related low-altitude frog R. chensinensis, and that the functional categories with accelerated evolutionary rates in R. kukunoris overlapped extensively with those detected along the P. erythrurus lineage. Conclusions: The mechanisms of high altitude adaptation in P. erythrurus were tentatively inferred. By comparing two pairs of low- and high-altitude poikilothermic species, we found that similar functional categories had undergone positive selection in high altitude-dwelling Phrynocephalus and Rana lineages, indicating that similar mechanisms of adaptation to high altitude might have evolved in both genera. Our findings provide important guidance for future functional studies on high altitude adaptation in poikilothermic animals.

研究背景：栖息于高海拔环境的生物必须克服三大环境挑战：低氧（hypoxia）、低温与强紫外线辐射。目前针对上述适应性挑战的分子机制研究主要集中在内温动物（endothermic organisms），而变温动物（poikilothermic species）相关研究则相对匮乏。本研究针对两种亲缘关系较近的蜥蜴——高海拔栖居的红尾沙蜥（Phrynocephalus erythrurus）与低海拔栖居的普氏沙蜥（P. putjatia）进行深度转录组测序，旨在鉴定受正向选择的候选基因，并探索变温动物向高海拔生活的趋同进化适应机制。
研究结果：通过Illumina测序平台，每个物种均获得超过7000万条序列读段。经从头组装（de novo assembly），红尾沙蜥与普氏沙蜥分别得到56845条和63140条转录本（transcripts）。红尾沙蜥的Ka/Ks比值高于普氏沙蜥，表明该高海拔蜥蜴支系的进化速率更快。在红尾沙蜥支系中，共检测到206个进化速率加快的基因本体（gene ontology, GO）类别，以及43个候选正向选择基因。其中部分GO类别所对应的功能与低氧应答、能量代谢及紫外线损伤应答相关。本研究还发现，高海拔蛙类青海湖蛙（Rana kukunoris）的Ka/Ks比值高于亲缘关系较近的低海拔蛙类中国林蛙（Rana chensinensis），且青海湖蛙中进化速率加快的功能类别与红尾沙蜥支系中检测到的类别存在广泛重叠。
研究结论：本研究初步推断了红尾沙蜥的高海拔适应机制。通过对比两对低海拔-高海拔变温动物物种，我们发现高海拔栖居的沙蜥属（Phrynocephalus）与蛙属（Rana）支系中，相似的功能类别均经历了正向选择，表明这两个属的物种可能演化出了相似的高海拔适应机制。本研究结果为未来变温动物高海拔适应的功能研究提供了重要指导。