Abstract
BackgroundT. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large economic losses. Understanding of the cold-tolerance mechanisms of this species is still limited. Integrated application of multi-omics research can provide a wealth of information to help us improve our understanding of low-temperature tolerance in fish.ResultsTo gain a comprehensive and unbiased molecular understanding of cold-tolerance in T. fasciatus, we characterized mRNA-seq and metabolomics of T. fasciatus livers using Illumina HiSeq 2500 and UHPLC-Q-TOF MS. We identified 2544 up-regulated and 2622 down-regulated genes in the liver of T. fasciatus. A total of 40 differential metabolites were identified, including 9 down-regulated and 31 up-regulated metabolites. In combination with previous studies on proteomics, we have established an mRNA-protein-metabolite interaction network. There are 17 DEMs (differentially-expressed metabolites) and 14 DEGs-DEPs (differentially co-expressed genes and proteins) in the interaction network that are mainly involved in fatty acids metabolism, membrane transport, signal transduction, and DNA damage and defense. We then validated a number of genes in the interaction network by qRT-PCR. Additionally, a number of SNPs (single nucleotide polymorphisms) were revealed through the transcriptome data. These results provide key information for further understanding of the molecular mechanisms of T. fasciatus under cold stress.ConclusionThe data generated by integrated application of multi-omics can facilitate our understanding of the molecular mechanisms of fish response to low temperature stress. We have not only identified potential genes and SNPs involved in cold tolerance, but also show that some nutrient metabolites may be added to the diet to help the overwintering of T. fasciatus.
Highlights
T. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large economic losses
The enrichment of arachidonic acid (ARA) and docosahexaenoic acid (DHA) is mainly related to AcylCoA desaturase (ACAD) [31], an enzyme involved in maintaining the balance between saturation and unsaturation of fatty acids
Down-regulation of this G protein would undoubtedly affect the metabolism of ARA. These results indicate that the metabolism of ARA in T. fasciatus subjected to low-temperature stress is regulated by various pathways and genes
Summary
T. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large economic losses. Wen et al BMC Genomics (2019) 20:563 producing temperature-specific isozymes [7], altering the content of membrane lipid and the degree of fatty acid unsaturation [8], recruiting different muscle fiber types [9], synthesizing molecular chaperones [10], and altering mitochondrial densities and their properties [11]. This amount of information is very limited for a comprehensive understanding of the changes in the organisms. The molecular mechanisms of teleost’s response to low-temperature stress have not yet been analyzed using multi-omics
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