Transcriptional differences provide insight into environmental acclimatization in wild amur ide (Leuciscus waleckii) during spawning migration from alkalized lake to freshwater river

Baohua Chen; Jian Xu; Jun Cui; Fei Pu; Wenzhu Peng; Lin Chen; Peng Xu

doi:10.1016/j.ygeno.2018.11.007

Transcriptional differences provide insight into environmental acclimatization in wild amur ide (Leuciscus waleckii) during spawning migration from alkalized lake to freshwater river

Genomics. 2019 May;111(3):267-276. doi: 10.1016/j.ygeno.2018.11.007. Epub 2018 Nov 13.

Authors

Baohua Chen¹, Jian Xu², Jun Cui³, Fei Pu⁴, Wenzhu Peng⁵, Lin Chen⁵, Peng Xu⁶

Affiliations

¹ Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen 361102, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde 352103, China.
² Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
³ Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China.
⁴ Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen 361102, China; State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde 352103, China.
⁵ Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen 361102, China.
⁶ Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen 361102, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde 352103, China. Electronic address: xupeng77@xmu.edu.cn.

PMID: 30445216
DOI: 10.1016/j.ygeno.2018.11.007

Abstract

Amur ide (Leuciscus waleckii) inhabits alkaline water in Lake Dali Nur and migrates to fresh water river for spawning every year. To investigate the potential genetic mechanisms underlying their alkaline acclimation, adaptation, and spawning migration, we performed differential gene expression analysis using high-throughput RNA-Seq data from liver of Amur ide samples collected before and after spawning migration. First, the short RNA-Seq reads were de novo assembled into 44,318 contigs, and provided the transcriptome reference sequences. Differential gene expression analysis identified 2575 genes with significant differential expression (p-value ≤.01, log2-fold-change ≥2). GO enrichment and KEGG pathway analyses were subsequently performed to determine gene functions and regulation. The results indicated that there were numerous differentially expressed genes involved in acid-base regulation, nitrogenous waste excretion, sexual maturation and reproduction, and stress response. These results provide fundamental information for further analyses of the physiological and molecular mechanisms underlying Amur ide alkaline acclimation, adaptation, and spawning migration.

Keywords: Amur ide; Gene expression; Leuciscus waleckii; RNA-Seq; Spawning migration; Transcriptome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Acclimatization*
Animal Migration*
Animals
Cyprinidae / genetics*
Cyprinidae / physiology
Lakes
Rivers
Transcriptome*