- Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb ( Puntius tetrazona. - Background: Tropical stenothermal fish exhibit special tolerance and response to cold stress. - However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. - tetrazona to low temperature, fish were exposed to increasing levels of acute cold stress. - Histopathological analysis showed that the brain, gill, liver and muscle tissues appeared serious damage after cold stress (13 °C). - There were 23,743 differently expressed genes (DEGs) been filtered from four pairs of tissues (brain, gill, liver and muscle) between these cold stress and control groups. - Our results suggested that ubiquitin- mediated protein degradation might be necessary for tropical stenothermal fish coping with acute cold stress. - These results suggested that the expression of the molecular chaperones HSP70 and CIRBP in P.. - tetrazona might play a critical role in coping with acute cold stress.. - Novel findings about tropical stenothermal fish under cold stress (such as HSP70 and CIRBP genes) are presented here. - This study contributes new insights into the molecular mechanisms of tropical stenothermal species response to acute cold stress.. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - A conservative responsive mechanism exists in different fish species under long-term low temperature and acute cold stress. - Also, ubiquitination-related genes are significantly expressed in temperate fish such as Cyprinus carpio [3–5], tropical fish such as Danio rerio [6, 7] and other fishes [8–11] when exposed to acute cold stress.. - Genes related to the regulation of peptidase activity, microtubule, cytoplasmic and cellular metabolic processes are involved in the responding to heat stress in barramundi muscle tissue [13]. - However, there has been no systematic study of the molecular mechanism underlying cold stress response in tiger barb.. - 2) identify the genes that were differently expressed under cold stress.. - Our results have potential applications in the breeding of cold-resistant tiger barb species for aquaculture.. - During spawning season, males exhibit bright red (nup- tial coloration) in the dorsal fin, ventral fin, caudal fin and snout (Fig. - tetrazona under a gradient cold stress were thus achieved (Fig. - 2c), the cells in the gill tissue of the COLD group showed shrinkage membrane contraction and even fracture (Fig. - 2e), severe fatty degeneration was in- duced in the hepatocytes of COLD group fish (Fig. - The myofibers of the CTRL group fish muscle was cov- ered by sarcolemma with well-arranged myofibrils in the sarcoplasm (Fig. - 2g), while the myofibrils were disorga- nized and irregular in the myofibers of COLD group fish muscle (Fig. - In the present study, the squares of the Pearson correlation co- efficient (R 2 values) fore gene expression values between biological replicates were larger than 0.8, indicating the high repeatability of biological replicates. - Meanwhile, the R 2 values between most differ- ent tissues were less than 0.5, which suggested less simi- larity in the gene expression patterns of multi-tissues (Supplementary Fig. - DEGs in multi-tissues under acute cold stress. - A total of 7771 DEGs consisting of 4418 up regulated genes (56.9%) and 3353 down regulated genes (43.1%) were verified in the gill tissue. - There were 4632 unigenes expressed differently in the liver tissue, including 1830 up regulated genes (39.5% of the total) and 2802 down regulated genes (60.5. - tetrazona under gradient cold stress. - e the logistic fit curve of survival rate under gradient cold stress. - Cold-induced DEGs in the brain, gill, liver and muscle shared some common ground (Fig. - The top 10 significantly enriched KEGG pathways (based on Padj value) in each tissue were reported in the Table 2 De novo transcriptome assembly assessment results. - Cold-induced DEGs in gill were mostly enriched in the immune system. - a the numbers of DEGs in multi-tissues after cold stress. - b the venn diagram of DEGs in multi-tissues after cold stress. - The expression levels of CUL9 increased under differ- ent cold temperatures in the gill, liver and particularly in muscle (up to 8-fold change relative to the control group). - The expression of TULP4 was induced signifi- cantly in the liver, followed by the gill and muscle under acute cold stress. - The expression of WWP2 was more sensitive to acute cold stress in the gill rather than in the brain or the liver. - The acute cold-induced expression of USP4 was found mainly in the muscle and the brain (Fig. - 6 Radar analysis of the temperature-dependent tissue-specific expression of ubiquitylation/deubiquitylation-related genes. - in the brain (77.7-fold) and the muscle (16.7-fold) after acute 13 °C cold stress (Padj <. - Our qPCR results confirmed this significant difference in the brain and the muscle with a up-regulation of 18.6 and 15.0 fold (P <. - Both the RNA-seq and qPCR data showed a weak increased expression in the liver after cold stress. - How- ever, the opposite expression trend was found in gill tis- sue using two methods, and one possible reason might be the low absolute expression levels in the gill (Fig. - Though only the expression of the gene encoding cold in- ducible RNA binding protein coding gene (CRIBP) in the brain (3.9-fold) and gill (2.9-fold) tissues was significantly induced by acute cold stress (13 °C) according to our RNA- seq data (Padj <. - 0.05), the expression levels of CRIBP were up regulated significantly in the brain, gill, liver and muscle tissues with and 2.8 fold after acute cold stress based on qPCR results (P <. - Cold stress is indicated by the decayed nup- tial coloration in P. - Decayed nuptial color- ation under mild cold stress (21 °C) indicates adverse ef- fects on health conditions and mating choice. - Muscle [24], gill [25], liver and brain [26] are the main target or- gans of cold stress in fish. - tetrazona suffer ser- ious damage under severe cold stress (13 °C).. - These non-coding genes were involved in the generat- ing of de novo transcriptome assembly.. - tetrazona revealed tissue-specific gene expression patterns and pathways in tiger barb respond- ing to acute cold stress. - The stenothermal tropical tiger barb shared some conserved cold-stress responsive mechanisms with extreme stenothermal fish, euryther- mal fish and other vertebrates. - Genes encoding proteins involved in protein biosyn- thesis and folding are over expressed in extreme stenother- mal fish compared to eurythermal fish for the adaption to chronic cold stress. - High protein consumption results in enriched transcripts of genes involved in the ubiquitin- mediated protein degradation pathway. - A transcriptome analysis of the Antarctic toothfish, Dissostichus mawsoni [31] showed that genes encoding proteins related to protein biosynthesis, folding and degradation are up-regulated in the cold-adapted transcriptome when compared with the tropical species zebrafish D. - Transcriptional profiling re- vealed that steroid biosynthesis, fatty acid biosynthesis and degradation in liver, fatty acids elongation and bio- synthesis of unsaturated fatty acids in muscle and fatty acid biosynthesis in the gill were all enriched after cold stress. - This study suggested that saturated/unsaturated fatty acids were involved in the response to acute cold stress in P. - biosynthesis, arginine and proline metabolism in the brain. - tryptophan metabolism, glycine, serine and threo- nine metabolism in the liver. - arginine biosynthesis, ala- nine, aspartate and glutamate metabolism in the muscle.. - Our results were consistent with observations in the common carp, whose gene expression in the glycolysis pathway increased under cold stress [5]. - The amino acid metabolism and glycometa- bolism in different fish tissues under cold stress have been reported, including in Larimichthy crocea [9], O.. - This study also showed that DEGs in the brain were classified into circadian regulation and circadian rhythm terms. - Transcriptional profiling of brain tissue revealed that the abundance of mRNA related to circadian regula- tion of gene expression might be driven by cold stress in P. - Our study also indicted the expression of the CIRBP gene in multi-tissues of P. - tetrazona and the up regula- tion under acute cold stress. - Our data indicated a common molecular response to cold stress in tropical stenothermal fish and other vertebrates.. - Additonally, the transcriptomic analysis in the present study revealed a specific cold-stress responsive mechan- ism in stenothermal tropical fish. - Our study validated the inducible expression of HSP70 in the brain and muscle tissues of P. - tetrazona under acute cold stress (13 °C), refreshing the perception of HSP genes expres- sion in tropical stenothermal fish coping with cold stress. - tetrazona under cold stress. - tetrazona coping with acute cold stress.. - Our study suggested that ubiquity- lation/deubiquitylation was prevalently-induced in tiger barb with tissue-specific ligases and substrates after acute cold stress. - Our data sup- plements the molecular mechanisms of tropical steno- thermal fish responding to low temperature stress, giving a hint to the specific molecular responses to cold stress in tropical stenothermal species compared to ex- treme stenothermal fish and eurythermal fish. - More de- tailed and comprehensive response mechanisms in multi-tissues from tropical stenothermal fish in response to cold stress deserve further research.. - Fish acclimation and acute cold stress. - The temperature was set to 27 ± 0.5 °C the first day, and descended 2 °C at each of 24 h. - The water temperature was monitored to keep it at set value±0.5 °C during the whole cold stress experiment.. - De novo transcriptome assembled in the study was used as a reference. - For DEG analysis between control and cold stress groups in multi-tissues, the DESeq soft- ware [76] was applied based on readcounts (from gene expression level analysis, Padj <. - The funding bodies had no role in the design of the study, data collection, analysis, interpretation of data, or preparation of the manuscript.. - The raw sequences were deposited in the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA) database (http://www.ncbi.nlm.. - Liver transcriptome sequencing and de novo annotation of the large yellow croaker (Larimichthy crocea) under heat and cold stress.. - Physiological responses to cold stress in the gills of discus fish (Symphysodon aequifasciatus) revealed by conventional biochemical assays and GC-TOF-MS metabolomics. - Effects of cold shock on responses of Phosphomonoesters and Free amino acids in phospholipid-rich organs in the Amur sleeper Perccottus Glehni. - Comprehensive transcriptome data for endemic Schizothoracinae fish in the Tibetan Plateau. - Different environmental temperatures affect amino acid metabolism in the eurytherm teleost Senegalese sole (Solea senegalensis Kaup, 1858) as indicated by changes in plasma metabolites.. - Temperature regulates transcription in the zebrafish circadian clock. - Recent progress in the research of cold-inducible RNA- binding protein. - Variation in the heat shock response and its implication for predicting the effect of global climate change on species' biogeographical distribution ranges and metabolic costs. - Expression analysis of heat shock genes in the skin, spleen and blood of common carp (Cyprinus carpio) after cadmium exposure and hypothermia. - HSP70, the earliest- induced gene in the zebrafish retina during optic nerve regeneration: its role in cell survival. - Physiological responses and HSP70 mRNA expression of GIFT strain of Nile tilapia (Oreochromis niloticus )under cold stress. - The HSP70 heat shock response in the Antarctic fish Harpagifer antarcticus. - Different rrelationship between hsp70 mRNA and hsp70 levels in the heat shock response of two salmonids with dissimilar temperature preference. - Diversity of degradation signals in the ubiquitin- proteasome system. - Regulatory mechanisms involved in the control of ubiquitin homeostasis
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