Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
Center for Advanced Retinal and Ocular Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Fish Shellfish Immunol. 2020 Feb;97:587-592. doi: 10.1016/j.fsi.2019.12.082. Epub 2019 Dec 28.
Recent genome-wide studies have begun to elucidate the genomic basis of hypoxia, long-term cold and high saline and alkaline adaptation in highland fish, and a number of key genes contributed to its highland adaptation were identified. An increasing number of studies indicated that immune genes of Tibetan endemic fish species underwent positive selection towards functional shift, while the insight into immune gene repertoire of Tibetan highland fishes from genome-wide studies has largely lagged behind. In this study, we performed one of the first comparative genomics study in particular focusing on the signatures of immune genes in a highland fish, Gymnocypris przewalskii based on immune-relevant tissue transcriptome assemblies. We identified seven putative rapidly evolving immune genes with elevated molecular evolutionary rate (dN/dS) relative to lowland fish species. Using tissue-transcriptome data, we found most of rapidly evolving immune genes were broadly expressed in head-kidney, spleen, gills and skin tissues, which significantly enriched for complement activation and inflammatory response processes. In addition, we found a set of complement activation related genes underwent accelerated evolution and showed consistently repressed expression patterns in response to parasite Ichthyophthirius multifiliis infection. Moreover, we detected a number of immune genes involved in adaptive immune system exhibited distinct signature of upregulated expression patterns after parasite infection. Taken together, this study provided putative transcriptomic signatures of rapidly evolving immune genes, and will gain the insight into Schizothoracine fish adaptation to high-altitude extreme aquatic environments including diversified pathogen challenge.
最近的全基因组研究开始阐明高原鱼类对低氧、长期寒冷、高盐和碱性的适应的基因组基础，并鉴定出一些有助于其高原适应的关键基因。越来越多的研究表明，西藏特有鱼类的免疫基因经历了功能转变的正选择，而从全基因组研究角度对西藏高原鱼类免疫基因库的了解却大大滞后。在这项研究中，我们进行了首次比较基因组学研究之一，特别关注高原鱼类——青海湖裸鲤（Gymnocypris przewalskii）的免疫基因特征，该研究基于与免疫相关的组织转录组组装。我们鉴定了七个具有相对低地鱼类更高的分子进化率（dN/dS）的假定快速进化的免疫基因。使用组织转录组数据，我们发现大多数快速进化的免疫基因在头肾、脾脏、鳃和皮肤组织中广泛表达，这些组织显著富集补体激活和炎症反应过程。此外，我们发现一组补体激活相关基因经历了加速进化，并在寄生虫多子小瓜虫（Ichthyophthirius multifiliis）感染时表现出一致的抑制表达模式。此外，我们检测到一些参与适应性免疫系统的免疫基因在寄生虫感染后表现出明显的上调表达模式特征。总之，本研究提供了快速进化的免疫基因的假定转录组特征，并深入了解了裂腹鱼类对包括多样化病原体挑战在内的高原极端水生环境的适应。
