Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments
Abstract 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 uncov...
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Nature Portfolio
2021-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-84652-5 |
| _version_ | 1818995405773340672 |
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| author | Shuangyi Wang Youyi Kuang Liqun Liang Bo Sun Xuefei Zhao Limin Zhang Yumei Chang |
| author_facet | Shuangyi Wang Youyi Kuang Liqun Liang Bo Sun Xuefei Zhao Limin Zhang Yumei Chang |
| author_sort | Shuangyi Wang |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-20T21:13:20Z |
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| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-20T21:13:20Z |
| publishDate | 2021-03-01 |
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| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-fb93327e123f4a2f9fb49ce9b46372712022-12-21T19:26:29ZengNature PortfolioScientific Reports2045-23222021-03-0111111410.1038/s41598-021-84652-5Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environmentsShuangyi Wang0Youyi Kuang1Liqun Liang2Bo Sun3Xuefei Zhao4Limin Zhang5Yumei Chang6National and Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesNational and Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesNational and Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesNational and Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesNational and Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesNational and Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesNational and Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesAbstract 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.https://doi.org/10.1038/s41598-021-84652-5 |
| spellingShingle | Shuangyi Wang Youyi Kuang Liqun Liang Bo Sun Xuefei Zhao Limin Zhang Yumei Chang Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments Scientific Reports |
| title | Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments |
| title_full | Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments |
| title_fullStr | Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments |
| title_full_unstemmed | Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments |
| title_short | Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments |
| title_sort | resequencing and snp discovery of amur ide leuciscus waleckii provides insights into local adaptations to extreme environments |
| url | https://doi.org/10.1038/s41598-021-84652-5 |
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