Genomic basis of adaptive evolution

The survival of amur ide (leuciscus waleckii) in an extremely alkaline environment

Jian Xu, Jiong Tang Li, Yanliang Jiang, Wenzhu Peng, Zongli Yao, Baohua Chen, Likun Jiang, Jingyan Feng, Peifeng Ji, Guiming Liu, Zhanjian "John" Liu, Ruyu Tai, Chuanju Dong, Xiaoqing Sun, Zi Xia Zhao, Yan Zhang, Jian Wang, Shangqi Li, Yunfeng Zhao, Jiuhui Yang & 2 others Xiaowen Sun, Peng Xu

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

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 50mmol/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.

Original languageEnglish (US)
Pages (from-to)145-159
Number of pages15
JournalMolecular Biology and Evolution
Volume34
Issue number1
DOIs
StatePublished - 2017
Externally publishedYes

Fingerprint

alkaline environment
genomics
Lakes
genome
Genome
teleost
lakes
Population
lake
Fishes
unfolded protein response
genome assembly
Unfolded Protein Response
Egg Proteins
egg proteins
Natriuretic Peptides
protein
terminal repeat sequences
Peptide Receptors
harbors (waterways)

Keywords

  • Acid-base regulation
  • Adaptation
  • Alkaline
  • Genome
  • Leuciscus waleckii
  • Urea excretion

ASJC Scopus subject areas

  • Medicine(all)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Genomic basis of adaptive evolution : The survival of amur ide (leuciscus waleckii) in an extremely alkaline environment. / Xu, Jian; Li, Jiong Tang; Jiang, Yanliang; Peng, Wenzhu; Yao, Zongli; Chen, Baohua; Jiang, Likun; Feng, Jingyan; Ji, Peifeng; Liu, Guiming; Liu, Zhanjian "John"; Tai, Ruyu; Dong, Chuanju; Sun, Xiaoqing; Zhao, Zi Xia; Zhang, Yan; Wang, Jian; Li, Shangqi; Zhao, Yunfeng; Yang, Jiuhui; Sun, Xiaowen; Xu, Peng.

In: Molecular Biology and Evolution, Vol. 34, No. 1, 2017, p. 145-159.

Research output: Contribution to journalArticle

Xu, J, Li, JT, Jiang, Y, Peng, W, Yao, Z, Chen, B, Jiang, L, Feng, J, Ji, P, Liu, G, Liu, ZJ, Tai, R, Dong, C, Sun, X, Zhao, ZX, Zhang, Y, Wang, J, Li, S, Zhao, Y, Yang, J, Sun, X & Xu, P 2017, 'Genomic basis of adaptive evolution: The survival of amur ide (leuciscus waleckii) in an extremely alkaline environment', Molecular Biology and Evolution, vol. 34, no. 1, pp. 145-159. https://doi.org/10.1093/molbev/msw230
Xu, Jian ; Li, Jiong Tang ; Jiang, Yanliang ; Peng, Wenzhu ; Yao, Zongli ; Chen, Baohua ; Jiang, Likun ; Feng, Jingyan ; Ji, Peifeng ; Liu, Guiming ; Liu, Zhanjian "John" ; Tai, Ruyu ; Dong, Chuanju ; Sun, Xiaoqing ; Zhao, Zi Xia ; Zhang, Yan ; Wang, Jian ; Li, Shangqi ; Zhao, Yunfeng ; Yang, Jiuhui ; Sun, Xiaowen ; Xu, Peng. / Genomic basis of adaptive evolution : The survival of amur ide (leuciscus waleckii) in an extremely alkaline environment. In: Molecular Biology and Evolution. 2017 ; Vol. 34, No. 1. pp. 145-159.
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AU - Chen, Baohua

AU - Jiang, Likun

AU - Feng, Jingyan

AU - Ji, Peifeng

AU - Liu, Guiming

AU - Liu, Zhanjian "John"

AU - Tai, Ruyu

AU - Dong, Chuanju

AU - Sun, Xiaoqing

AU - Zhao, Zi Xia

AU - Zhang, Yan

AU - Wang, Jian

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AU - Zhao, Yunfeng

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AU - Sun, Xiaowen

AU - Xu, Peng

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