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Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments

文献类型： 外文期刊

作者： Wang, Shuangyi 1 ; Kuang, Youyi 1 ; Liang, Liqun 1 ; Sun, Bo 1 ; Zhao, Xuefei 1 ; Zhang, Limin 1 ; Chang, Yumei 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Heilongjiang River Fisheries Res Inst, Natl & Local United Engn Lab Freshwater Fish Bree, Harbin 150070, Peoples R China

2.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai 200000, Peoples R China

3.Northeast Forestry Univ, Coll Wildlife & Protected Area, Harbin 150040, Peoples R China

期刊名称：SCIENTIFIC REPORTS （ 影响因子：4.379； 五年影响因子：5.133 ）

ISSN： 2045-2322

年卷期： 2021 年 11 卷 1 期

页码：

收录情况： SCI

摘要： Amur ide (Leuciscus waleckii), a Cyprinid species, is broadly distributed in Northeast Asia. Different from its freshwater counterparts, the population in Lake Dali Nor has a strong alkalinity tolerance and can adapt to extremely alkali-saline water with bicarbonate over 50 mmol/L. To uncover the genetic basis of its alkaline adaptation, three populations, including one alkali form from Lake Dali Nor (DL), one freshwater form from its adjacent sister Lake Ganggeng Nor (GG), and one freshwater form from its historical origin, namely, the Songhua River (SH), were analyzed using genome resequencing technology. A total of 679.82 Gb clean data and 38,091,163 high-quality single-nucleotide polymorphism (SNP) loci were detected in the three populations. Nucleotide diversity and population structure analysis revealed that the DL and GG populations have lower nucleotide diversities and different genetic structures than those of the SH population. Selective sweeping showed 21 genes involved in osmoregulatory regulation (DLG1, VIPR1, AKT1, and GNAI1), inflammation and immune responses (DLG1, BRINP1, CTSL, TRAF6, AKT1, STAT3, GNAI1, SEC22b, and PSME4b), and cardiorespiratory development (TRAF6, PSME4b, STAT3, AKT1, and COL9A1) to be associated with alkaline adaption of the DL population. Interestingly, selective pressure (CodeML, MEME, and FEL) methods identified two functional codon sites of VIPR1 to be under positive selection in the DL population. The subsequent 3D protein modeling confirmed that these selected sites will incur changes in protein structure and function in the DL population. In brief, this study provides molecular evidence of population divergence and alkaline adaptation, which will be very useful for revealing the genetic basis of alkaline adaptation in Amur ide.

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