Gene Expression Profile and Co-Expression Network of Pearl Gentian Grouper under Cold Stress by Integrating Illumina and PacBio Sequences

Abstract

Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying cold stress remains largely elusive. This study thus investigated the liver transcriptomic responses of pearl gentian grouper by comparing the gene expression of cold stress groups (20, 15, 12, and 12 °C for 6 h) with that of control group (25 °C) using PacBio SMRT-Seq and Illumina RNA-Seq technologies. In SMRT-Seq analysis, a total of 11,033 full-length transcripts were generated and used as reference sequences for further RNA-Seq analysis. In RNA-Seq analysis, 3271 differentially expressed genes (DEGs), two low-temperature specific modules (tan and blue modules), and two significantly expressed gene sets (profiles 0 and 19) were screened by differential expression analysis, weighted gene co-expression networks analysis (WGCNA), and short time-series expression miner (STEM), respectively. The intersection of the above analyses further revealed some key genes, such as PCK, ALDOB, FBP, G6pC, CPT1A, PPARα, SOCS3, PPP1CC, CYP2J, HMGCR, CDKN1B, and GADD45Bc. These genes were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and endocrine system pathways. All these pathways were linked to biological functions relevant to cold adaptation, such as energy metabolism, stress-induced cell membrane changes, and transduction of stress signals. Taken together, our study explores an overall and complex regulation network of the functional genes in the liver of pearl gentian grouper, which could benefit the species in preventing damage caused by cold stress.

The MicroRNAs-Transcription Factors-mRNA Regulatory Network Plays an Important Role in Resistance to Cold Stress in the Pearl Gentian Grouper

“…The experimental process (Figure 1A) included temporary fish culture, cold stress treatment, liver tissue collection under anesthesia, and total RNA extraction from samples and was performed following the methods described in our previous transcriptome study (Miao et al, 2021). Briefly, 150 healthy juveniles of the pearl gentian grouper hatched from Hainan (northern South China Sea, China) breeding parents were equally divided into three parallel experimental tanks.…”

“…This obviously limits the breeding scope and environment of this grouper, which is not conducive to the expansion of its aquaculture industry. For this reason, we previously analyzed changes in the liver transcriptome of pearl gentian grouper under cold stress by integrating PacBio SMRT-Seq and Illumina RNA-Seq technologies and successfully screened various cold-related genes and biological pathways; our results indicated that energy homeostasis may play a crucial role in physiological responses to cold stress in the species (Miao et al, 2021). However, the regulatory relationships and dynamics of these genes are still unclear, and the construction of miRNA-TF-mRNA network is necessary to clarify regulatory mechanisms at the pre-and post-transcriptional levels underlying the transient response to low-temperature stress in this grouper and to narrow the screening of cold-related candidate genes.…”

Transcriptomic Networks Reveal the Tissue-Specific Cold Shock Responses in Japanese Flounder (Paralichthys olivaceus)

“…Mitochondrial ribosome-associated GTPase 2 (GTPBP5) plays a role in the regulation of the mitochondrial ribosome assembly and of translational activity, all suggesting the inhibited function of the “cell cycle” and “cell division” [ 49 , 50 , 51 , 52 ]. In the livers of fish, high-temperature stress may affect apoptosis, DNA replication, protein metabolism, energy metabolism, lipid metabolism, immune, cell cycle, protein processing, and transport, as well as antioxidative responses [ 53 , 54 , 55 ], while low-temperature stress may affect signaling transduction, membrane fluidity, lipid metabolism, antioxidative responses, ion binding, macromolecule catabolism, mitochondrial enzymes related to transport, carbohydrate metabolism, and cell cycle endocrine system [ 56 , 57 ]. Interestingly, inositol polyphosphate-5-phosphatase A (INPP5A) and phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (INPP5J) were interlinked as the up- and downregulated DEGs in the network, respectively ( Figure 4 and Figure 5 ), which may suggest the effects of membrane fluidity and lipid metabolism involved in the modulation of inositol function and the influence of cell migration, adhesion, and polarity in P. olivaceus livers under cold shock [ 58 ].…”

Physiological, metabolomic, and transcriptomic reveal metabolic pathway alterations in Gymnocypris przewalskii due to cold exposure

“…Such a strategy may contribute to maintaining contractile function in the trout heart during cold acclimation [ 97 ]. In the pearl gentian grouper, cardiac muscle contraction was detected based on RNA-seq results and could be physiologically adjusted to reduce damage and maintain essential life functions under cold stress [ 98 ]. Herein, we found that the cardiac muscle contraction pathway was significantly enriched in the heart DEGs and that key genes, including cytochrome c oxidase subunit 7A2 gene ( Cox7a2 ) and cytochrome c oxidase subunit 5A gene ( Cox5a ), were upregulated by cold stress.…”