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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Autores principales:	Shuangyi Wang, Youyi Kuang, Liqun Liang, Bo Sun, Xuefei Zhao, Limin Zhang, Yumei Chang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fb93327e123f4a2f9fb49ce9b4637271
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spelling	oai:doaj.org-article:fb93327e123f4a2f9fb49ce9b46372712021-12-02T13:20:20ZResequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments10.1038/s41598-021-84652-52045-2322https://doaj.org/article/fb93327e123f4a2f9fb49ce9b46372712021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-84652-5https://doaj.org/toc/2045-2322Abstract 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.Shuangyi WangYouyi KuangLiqun LiangBo SunXuefei ZhaoLimin ZhangYumei ChangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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
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.
format	article
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
title	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_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_sort	resequencing and snp discovery of amur ide (leuciscus waleckii) provides insights into local adaptations to extreme environments
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fb93327e123f4a2f9fb49ce9b4637271
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Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments

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