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Mol Biol Evol. 2017 Jan;34(1):145-159. doi: 10.1093/molbev/msw230. Epub 2016 Oct 20.

Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment.

Author information

1
Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
2
State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, China.
3
Engineering Research Centre for Saline-alkaline Fisheries, East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Shanghai, China.
4
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
5
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL.
6
Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV.
7
Dalinor National Nature Reserve, Keshiketeng, Chifeng, China.
8
Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China xupeng77@xmu.edu.cn.
9
Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, China.

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 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.

KEYWORDS:

Leuciscus waleckii; acid–base regulation; adaptation; alkaline; genome; urea excretion

PMID:
28007977
PMCID:
PMC5854124
DOI:
10.1093/molbev/msw230
[Indexed for MEDLINE]
Free PMC Article

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