Xu Jian, Li Jiong-Tang, Jiang Yanliang, Peng Wenzhu, Yao Zongli, Chen Baohua, Jiang Likun, Feng Jingyan, Ji Peifeng, Liu Guiming, Liu Zhanjiang, Tai Ruyu, Dong Chuanju, Sun Xiaoqing, Zhao Zi-Xia, Zhang Yan, Wang Jian, Li Shangqi, Zhao Yunfeng, Yang Jiuhui, Sun Xiaowen, Xu Peng
Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, China.
Mol Biol Evol. 2017 Jan;34(1):145-159. doi: 10.1093/molbev/msw230. Epub 2016 Oct 20.
The Amur ide (Leuciscus waleckii) is a cyprinid fish that is widely distributed in Northeast Asia. The Lake Dali Nur population inhabits one of the most extreme aquatic environments on Earth, with an alkalinity up to 50 mmol/L (pH 9.6), thus providing an exceptional model with which to characterize the mechanisms of genomic evolution underlying adaptation to extreme environments. Here, we developed the reference genome assembly for L. waleckii from Lake Dali Nur. Intriguingly, we identified unusual expanded long terminal repeats (LTRs) with higher nucleotide substitution rates than in many other teleosts, suggesting their more recent insertion into the L. waleckii genome. We also identified expansions in genes encoding egg coat proteins and natriuretic peptide receptors, possibly underlying the adaptation to extreme environmental stress. We further sequenced the genomes of 10 additional individuals from freshwater and 18 from Lake Dali Nur populations, and we detected a total of 7.6 million SNPs from both populations. In a genome scan and comparison of these two populations, we identified a set of genomic regions under selective sweeps that harbor genes involved in ion homoeostasis, acid-base regulation, unfolded protein response, reactive oxygen species elimination, and urea excretion. Our findings provide comprehensive insight into the genomic mechanisms of teleost fish that underlie their adaptation to extreme alkaline environments.
黑龙江鳑鲏（Leuciscus waleckii）是一种鲤科鱼类，广泛分布于东北亚地区。达里诺尔湖种群栖息于地球上最极端的水生环境之一，碱度高达50 mmol/L（pH 9.6），因此为研究适应极端环境的基因组进化机制提供了一个特殊的模型。在此，我们构建了达里诺尔湖黑龙江鳑鲏的参考基因组组装。有趣的是，我们发现了不寻常的扩展长末端重复序列（LTRs），其核苷酸替换率高于许多其他硬骨鱼类，这表明它们是最近才插入到黑龙江鳑鲏基因组中的。我们还发现编码卵壳蛋白和利钠肽受体的基因发生了扩增，这可能是适应极端环境压力的基础。我们进一步对另外10个淡水个体和18个达里诺尔湖种群个体的基因组进行了测序，从这两个种群中总共检测到760万个单核苷酸多态性（SNP）。在对这两个种群的基因组扫描和比较中，我们确定了一组处于选择清除下的基因组区域，这些区域包含参与离子稳态、酸碱调节、未折叠蛋白反应、活性氧清除和尿素排泄的基因。我们的研究结果为硬骨鱼类适应极端碱性环境的基因组机制提供了全面的见解。
