基于基因组测序的中国特有金线鲃属鱼类洞穴适应机制和种群历史研究

As one of the Chinese endemic fish genera, Sinocyclocheilus is a representative group of species that can live in perpetual darkness of Karst Caves in southwestern of China, and it’s also the historical witness of the uplift of Qinghai-Tibet & Yunnan-Guizhou plateaus, as well as other synergetic geological events such as the formation and development of plateau lakes. This genus serves as an emerging and ideal cavefish model for its high phenotypic variation and species diversity. We have succeeded in reporting three genomes from three species of Sinocyclocheilus, where we found that a lot of genetic changes in the genome of cavefish would be the responses to cave adaptation, and we also revealed that there were close relationships between the population dynamics of Sinocyclocheilus species and their surrounding changes under the uplift of Qinghai-Tibet plateau. Based on the previous results, we wish to expand our research objects to four other Sinocyclocheilus species in this proposal. Two sister species (surface-dwelling S. maitianheensis and cave-restricted S. anophthalmus) will use for denovo genome sequencing to verify and detect more genetic changes in cavefishes and its corresponding mechanisms, and to further explore the possible common trend of life evolution in darkness. Two other close related species (Fuxianhu lake dwelling S. tingi and Yangzonghai lake dwelling S. yangzongensis) will use for genome resequencing to reconstruct the historical relationships between the population dynamics of these species and the significant geological events such as evolution of lakes in middle Yunnan province and river captures herein, when combined with the dataset from the previous reported genome of Dianchi lake dwelling S. grahami.

我国特有金线鲃属鱼类是洞穴生物的代表类群，同时也是青藏高原-云贵高原隆升、高原湖泊演化等地质事件的见证者。多变的表型多样性和丰富的物种多样性使其成为研究洞穴适应性进化、生物地理演化的理想素材。我们曾在国际上率先对3种金线鲃鱼类全基因组进行了解译，发现了一系列重要的遗传变异可能与其洞穴适应有关，揭示了金线鲃鱼类种群历史与青藏高原隆升以及高原湖泊演化具有密切联系。基于前期研究积累，本项目拟扩大研究范围对近缘的4种金线鲃鱼类进行基因组测序，即从头测序1对姐妹种（地表种-麦田河金线鲃和洞穴种-无眼金线鲃），以验证和发掘更多洞穴适应有关的基因变化及相应的遗传机制，探索生物在黑暗无光的极端环境下演化的共同趋势；对另外2个近缘种（抚仙湖的抚仙金线鲃和阳宗海的阳宗金线鲃）进行重测序，结合前期已获得的滇池金线鲃基因组数据，重建三种鱼类种群动态与上新世以来滇中地区湖泊演化及河流改道等重大历史事件之间的联系。

金线鲃属鱼类是我国特有的洞穴生物代表类群，主要分布于我国西南滇黔桂喀斯特地区。复杂多样的喀斯特环境造就了该属鱼类极其丰富的物种多样性和表型多样性。同时，也使其成为研究洞穴适应性进化、生物地理演化的理想素材。本课题主要基于基因组测序技术和比较基因组分析，对金线鲃属鱼类开展洞穴机制适应研究。同时，通过开展昼夜节律、游泳能力研究等行为学实验来验证金线鲃属鱼类表型多样性，并对其种群扩散情况进行探究。主要成果包含以下几个方面：（1）发现以犀角金线鲃和安水金线鲃为代表的洞穴金线鲃随着洞穴化程度的提高逐步发生了昼夜节律的弱化以至消失，同时活动强度也有明显降低。此外，头部表面神经丘数量也随着洞穴化程度的增高而降低。（2）对麦田河金线鲃和无眼金线鲃进行了基因组de novo组装，并结合前期已组装好的3种金线鲃基因组进行洞穴适应机制探究，发现一些节律、色素相关基因（如aaad, slc24a5）上的变异可能导致了洞穴金线鲃昼夜节律和皮肤色素的退化；此外，通过5种鱼类免疫相关基因进行差异表达分析，在地表种和洞穴种中发现一些与免疫相关的差异表达基因。（3）构建了滇池金线鲃染色体水平基因组。（4）发现不同生态型中金线鲃鱼类游泳能力存在差异，且同一物种成体和亚成体游泳能力也存在一定的差异。这些成果在一定程度上揭示了金线鲃属鱼类可能存在的洞穴适应的趋同进化或普遍机制。同时，为后续洞穴适应性研究与验证，为新的疾病研究模型的发展，以及地表经济种类物种保护、遗传育种等方面的工作奠定基础。