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

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

doi:10.3390/ani11113021

Yibo Zhang, Jingqian Wang + Show 9 more

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https://doi.org/10.3390/ani11113021

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Abstract

Simple SummaryHypoxia, which occurs frequently in aquaculture, can cause serious harm to all aspects of the growth, reproduction and metabolism of cultured fish. Due to the intolerance of Larimichthys crocea to hypoxia, Larimichthys crocea often floats head or even dies under hypoxic environment. However, the molecular mechanism of hypoxia tolerance in Larimichthys crocea has not been fully described. Therefore, the aim of this study was to explore the hub regulatory genes under hypoxic stress environment by transcriptome analysis of three key tissues (liver, blood and gill) in Larimichthys crocea. We identified a number of important genes that exercise different regulatory functions. Overall, this study will provide important clues to the molecular mechanisms of hypoxia tolerance in Larimichthys crocea.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.

Highlights

Oxygen is a key environmental factor for growth, development, and reproduction of various living organisms; as it is not soluble in water, the dissolved oxygen (DO) content of natural water is exceptionally low (~1/34th of that in air)
The results indicate that hub genes associated with hypoxia and reoxygenation stress may play important roles in identifying candidate biomarkers and understanding the molecular mechanisms of hypoxia tolerance
The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the adaptation strategy of L. crocea to hypoxia was significantly tissue-specific, with blood, gills, and liver associated with functional terms and pathways of oxygen transport, ion regulation, and energy metabolism, respectively, which corresponded to the physiological functions of the tissues as well

Summary

Introduction

Oxygen is a key environmental factor for growth, development, and reproduction of various living organisms; as it is not soluble in water, the dissolved oxygen (DO) content of natural water is exceptionally low (~1/34th of that in air). The DO levels in water bodies are susceptible to various natural and human-induced factors, resulting in aquatic animals often suffering from hypoxia effects on their growth, development, and reproduction [1,2]. Studies show that more than 400 hypoxia zones have emerged in the world’s oceans, covering thousands of square kilometers, with some offshore areas even becoming permanently hypoxic. Environmental factors such as climate change are set to exacerbate the problem [3,4,5,6]. The effects of hypoxia on aquatic animals have become a hot topic in academic research worldwide

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