Genetics Responses to Hypoxia and Reoxygenation Stress in Larimichthys crocea Revealed via Transcriptome Analysis and Weighted Gene Co-Expression Network

Yibo Zhang; Jie Ding; Cheng Liu; Shengyu Luo; Xinming Gao; Yuanjie Wu; Jingqian Wang; Xuelei Wang; Xiongfei Wu; Weiliang Shen; Junquan Zhu

doi:10.3390/ani11113021

Genetics Responses to Hypoxia and Reoxygenation Stress in Larimichthys crocea Revealed via Transcriptome Analysis and Weighted Gene Co-Expression Network

Animals (Basel). 2021 Oct 20;11(11):3021. doi: 10.3390/ani11113021.

Authors

Yibo Zhang^{1

2}, Jie Ding^{1

2}, Cheng Liu^{1

2}, Shengyu Luo¹, Xinming Gao¹, Yuanjie Wu¹, Jingqian Wang¹, Xuelei Wang², Xiongfei Wu², Weiliang Shen², Junquan Zhu¹

Affiliations

¹ Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, 169 South Qixing Road, Ningbo 315832, China.
² State Key Laboratory of Large Yellow Croaker Breeding, Ningbo Academy of Oceanology and Fishery, Juxian Road, Ningbo 315103, China.

Abstract

The large yellow croaker (Larimichthys crocea) is an important marine economic fish in China; however, its intolerance to hypoxia causes widespread mortality. To understand the molecular mechanisms underlying hypoxia tolerance in L. crocea, the transcriptome gene expression profiling of three different tissues (blood, gills, and liver) of L. crocea exposed to hypoxia and reoxygenation stress were performed. In parallel, the gene relationships were investigated based on weighted gene co-expression network analysis (WGCNA). Accordingly, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that several pathways (e.g., energy metabolism, signal transduction, oxygen transport, and osmotic regulation) may be involved in the response of L. crocea to hypoxia and reoxygenation stress. In addition, also, four key modules (darkorange, magenta, saddlebrown, and darkolivegreen) that were highly relevant to the samples were identified by WGCNA. Furthermore, some hub genes within the association module, including RPS16, EDRF1, KCNK5, SNAT2, PFKL, GSK-3β, and PIK3CD, were found. This is the first study to report the co-expression patterns of a gene network after hypoxia stress in marine fish. The results provide new clues for further research on the molecular mechanisms underlying hypoxia tolerance in L. crocea.

Keywords: Larimichthys crocea; WGCNA; hub genes; hypoxia; transcriptome.