title: Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment.
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.
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Jiong-Tang
authors.initials: JT
authors.lastname: Li
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Yanliang
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.|State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, China.
authors.forename: Wenzhu
authors.initials: W
authors.lastname: Peng
authors.affiliation: Engineering Research Centre for Saline-alkaline Fisheries, East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Shanghai, China.
authors.forename: Zongli
authors.initials: Z
authors.lastname: Yao
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Baohua
authors.initials: B
authors.lastname: Chen
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Likun
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Jingyan
authors.initials: J
authors.lastname: Feng
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Peifeng
authors.initials: P
authors.lastname: Ji
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Guiming
authors.initials: G
authors.lastname: Liu
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Ruyu
authors.initials: R
authors.lastname: Tai
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Chuanju
authors.initials: C
authors.lastname: Dong
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Sun
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Zi-Xia
authors.initials: ZX
authors.lastname: Zhao
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Shangqi
authors.initials: S
authors.lastname: Li
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Yunfeng
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Dalinor National Nature Reserve, Keshiketeng, Chifeng, China.
authors.forename: Jiuhui
authors.initials: J
authors.lastname: Yang
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Sun
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China xupeng77@xmu.edu.cn.|State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, China.|Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D001208:Asia; D005075:Biological Evolution; D003530:Cyprinidae / Q000235:genetics*; D019143:Evolution, Molecular; D000071251:Extreme Environments; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D056726:Genetic Association Studies; D023281:Genomics / Q000379:methods; D006863:Hydrogen-Ion Concentration; D060106:Lakes; D017422:Sequence Analysis, DNA / Q000379:methods; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome
keywords: Leuciscus waleckii; acid–base regulation; adaptation; alkaline; genome; urea excretion