Transcriptome and co-expression network analyses reveal the regulatory pathways and key genes associated with temperature adaptability in the yellow drum (Nibea albiflora)

Abstract

The yellow drum (Nibea albiflora) is an important marine economy fish, that is widely distributed in the coastal waters of the Northwest Pacific. To understand the molecular regulatory mechanism of the yellow drum under temperature stress, transcriptome analysis was performed under five temperature conditions (10 °C, 15 °C, 20 °C, 24 °C, 28 °C) in the present study. Compared with 20 °C, 163, 401, 276, and 372 differentially expressed genes (DEGs) were obtained at 10 °C, 15 °C, 24 °C and 28 °C, respectively. Gene Ontology (GO) analysis indicated that the DEGs were mainly involved in cellular processes, metabolic processes, catalytic activity, membrane and binding. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the temperature adaptive regulation of the yellow drum was mainly involved in signal transduction, metabolism, genetic information and protein processing. Weighted gene co-expression network analysis (WGCNA) showed that HMGB1, STAT4, Noct, C1q and CRT may be the key hub genes in the response of the yellow drum to temperature stress. In addition, 20 genes that may be associated with temperature stress were identified based on comparative analysis between the KEGG enrichment and the WGCNA results. Ten DEGs were selected for further validation using quantitative real-time PCR (qRT-PCR), and the results were consistent with the RNA-seq data. This study explored the transcriptional patterns of the yellow drum under temperature stress and provided fundamental information on the temperature adaptability of this species.

Keywords: Differentially expressed genes (DEGs); Nibea albiflora; Temperature stress; Transcriptome; WGCNA.