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Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus

ABSTRACT: we used next-generation sequencing technology to characterise mRNA-seq of control- and hypoxia-treated T. fasciatus livers to elucidate the molecular mechanisms of cold adaptation. We were able to find mRNA pairs using bioinformatics analysis.

ORGANISM(S): Takifugu fasciatus

PROVIDER: GSE129226 | GEO | 2020/04/10

REPOSITORIES: GEO

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Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus.

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Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus

Project description:Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus

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Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies

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Transcriptomic insights into differential cold tolerance of two tobacco cultivars

Project description:Purpose: we conducted a six time-point transcriptomic analysis using two tobacco cultivars with contrasting cold responses, Taiyan8 tobacco (TT, cold susceptibility) and Yanyan97 tobacco (YT, cold resistance). Methods: mRNA profiles of Tobacco seedlings from CK and cold-treated plants were generated by deep sequencing, in triplicate, usingIllumina Hiseq4500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with methods: hisat2 (v2.0.5), SAMtools (v1.9). StringTie (v1.3.4d) and FeatureCounts (v1.6.4) Results: We found that both cultivars had common mechanisms to cope with cold stress, including common differentially expressed genes (DEGs), similar time-point-related differential expression profile of genes, and similar NtCBF gene co-expression modules, suggesting conservation of adaptation strategies for cold responses. Importantly, we found that YT experienced DEGs even under normal growth condition and had less DEGs in early stage of cold stress (0.5-2 h) when compared to TT, reflecting occurrence of genotype-dependent gene transcription. Moreover, a gene co-expression module (brown) with stress-related genes up-regulated in YT instead of TT at late stage (4-8 h), which might contribute to contrasting phenotypic changes during cold stress between TT and YT. Conclusions: our study provides valuable resources for transcriptomic studies of cold responses in plants. It also helps to identify key cold responsive genes for genetic manipulation for breeding of tobacco cultivars in the future.

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The Effects of Regular Post-Exercise Cold Water Immersion on Gene Expression in Muscle Following 10-weeks of Strength Training

Project description:In this study, the primary objective was to characterise the impact of regular post-exercise (20 strength training sessions across 10 weeks) cold-water immersion (CWI) on mRNA expression. Secondary to this, the effect of regular post-exercise CWI on strength gains and post-exercise soreness was investigated. We used microarrays to detail the global effects of CWI on gene expression in vastus lateralis muscle tissue.

2016-08-16 | GSE85620 | GEO

Integrated multi-omics analysis provides insights into genome evolution and phosphorus deficiency adaptation in pigeonpea (<i>Cajanus cajan</i>).

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prp43 COLD SHIFT

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Expression data in Arabidopsis Col-0 with cold acclimation (CA) treatment and subsequent cold deacclimation (DA) treatment.

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2014-10-02 | GSE49796 | GEO

Loss of a-actinin-3 during human evolution provides superior cold resilience and muscle heat generation

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Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Phaseolus vulgaris L.

Project description:Cold tolerance of crop plants influences survival and productivity under low-temperature conditions. Elucidation of molecular mechanisms underlying low temperature tolerance could be helpful in breeding. In this study, based on transcriptome and metabolomic analysis, we successfully identified a number of candidate genes and metabolites involved in key biological pathways during cold stress response. During cold stress, a total of 22335 differentially expressed genes were detected in each group (093Cvs120C, 093Tvs120T, 093Cvs093T, 120Cvs120T), of which 12978 were up-regulated and 9357 were down-regulated. A total of 18,166 metabolites were detected and 7,670 metabolites were annotated, among which 654 were secondary metabolites with significant differences. Under cold stress, the petC gene in both common bean cultivars was down-regulated, which led to the decrease of photosynthetic efficiency. Transcriptome and metabolome results under cold stress showed that the synthesis pathways of various unsaturated fatty acids including alpha-linolenic acid were significantly up-regulated and their contents were enriched. In addition, leukotriene-A4 hydrolase in the catabolic pathway of 120 arachidonic acid was inhibited under cold stress. Furthermore, the content of arachidonic acid was increased. A variety of amino acids in both 093 and 120 were enriched under cold stress, which was beneficial to the resistance of bean to osmotic stress caused by cold stress. However, in addition to a few amino acids that were enriched together, 093 was mainly positively charged and 120 was negatively charged among the amino acids that were enriched differently. This is an interesting phenomenon that needs to be further studied. In addition, under cold stress, we found that genes in multiple metabolic pathways, including ABA, GA, JA and other hormone metabolism pathways, were differentially expressed in 093 and 120.

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