Transcriptome analysis of a heat-resistant jujube cultivar response to high temperature stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Ziziphus jujuba
PROVIDER: GSE136047 | GEO | 2020/10/02
REPOSITORIES: GEO
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Project description:Jujube (Ziziphus jujuba Mill.) is an economically and agriculturally significant fruit crop and is widely cultivated throughout the world. Heat stress has recently become one of the major abiotic stresses limiting plant growth and productivity. However, there are few studies on the transcriptome profiling of jujube subjected to heat stress. In this study, we analyzed the physiological and transcriptomic changes of heat-resistant jujube cultivar ‘HR’ and heat-sensitive cultivar ‘HS’ caused by high temperature stress. We statistically determined 984, 1468, 1727 and 2098 differentially expressed genes (DEGs) between ‘HR’ and ‘HS’ after 0, 1, 3, 5 d of heat stress, respectively. Gene Ontology (GO) enrichment analysis indicated that Aa great deal of heat-responsive genes were identified in these DEGs by Gene Ontology (GO) enrichment analysis. It suggests the distinct molecular mechanism of jujube response to heat stress. Furthermore, we validated the expression profiles of 12 candidates using qRT-PCR to further confirm the accuracy of the RNA-seq data. These results will advance our knowledge of the genes involved in the complex regulatory networks of heat stress and provide genetic resources for further improving the heat tolerance in jujube.
2020-10-02 | GSE136383 | GEO
Project description:Transcriptional profiling of pear tree comparing a resistant/tolerant cultivar with a susceptible cultivar to the Stemphylium vesicarium fungus Rocha' pear is an economically important portuguese Pyrus communis L. cultivar very susceptible to the Stemphylium vesicarium pathogenic fungus, the brown spot agent, causing huge decrease on fruit quality and yield production. Field control of brown spot disease is based in systemic application of antifungal chemicals with high economic costs and dramatic consequences to public health and environmental pollution. Plant-pathogen interactions involve a series of events encompassing constitutive and induced plant defence responses whose dissection has been a research target for control many crop diseases. The biosynthesis of cell wall polymers and antifungal compounds appear to be an efficient physical and chemical barrier to infection.To understand the molecular responses behind defence mechanisms of resistant/tolerant and susceptible cultivars of Pyrus communis L. to the S. vesicarium fungus, cDNA microarray technology was used to identify the genes differentially expressed along a time course leaf inoculation between 'Rocha' pear cultivar (a high susceptible cultivar) and 'Ercolini' pear cultivar (a resistant/tolerant pear cultivar). This study aims to contribute with information on the molecular mechanisms involved in host-pathogen interactions responsible for pear tree brown spot disease and resistance to Stemphylium vesicarium. Experimental condition: 'Ercolini' vs 'Rocha' (each experiment including 5 plants from each cultivar). 3 time-points: water-inoculation (T0h), 6 hours after inoculation with S. vesicarium (T6h) and 24 hours after inoculation with S. vesicarium. Biological replicates: 3 in each time-point. One replicate per array.
2011-07-02 | E-GEOD-30353 | biostudies-arrayexpress
Project description:Transcriptional profiling of pear tree comparing a resistant/tolerant cultivar with a susceptible cultivar to the Stemphylium vesicarium fungus Rocha' pear is an economically important portuguese Pyrus communis L. cultivar very susceptible to the Stemphylium vesicarium pathogenic fungus, the brown spot agent, causing huge decrease on fruit quality and yield production. Field control of brown spot disease is based in systemic application of antifungal chemicals with high economic costs and dramatic consequences to public health and environmental pollution. Plant-pathogen interactions involve a series of events encompassing constitutive and induced plant defence responses whose dissection has been a research target for control many crop diseases. The biosynthesis of cell wall polymers and antifungal compounds appear to be an efficient physical and chemical barrier to infection.To understand the molecular responses behind defence mechanisms of resistant/tolerant and susceptible cultivars of Pyrus communis L. to the S. vesicarium fungus, cDNA microarray technology was used to identify the genes differentially expressed along a time course leaf inoculation between 'Rocha' pear cultivar (a high susceptible cultivar) and 'Ercolini' pear cultivar (a resistant/tolerant pear cultivar). This study aims to contribute with information on the molecular mechanisms involved in host-pathogen interactions responsible for pear tree brown spot disease and resistance to Stemphylium vesicarium.
2011-07-02 | GSE30353 | GEO
Project description:We used microarray to study the transcriptome response of wheat flag leaves to heat stress (40℃) In order to study the transcriptome response of wheat flag leaf to heat stress, wheat cultivar ‘TAM 107’ plants were subjected to heat stress (40℃). After 1 hour of stress, flag leaves were sampled from both stressed and control plants and were used for microarray analysis.
2015-08-13 | E-GEOD-60351 | biostudies-arrayexpress
Project description:Asian cultivated rice (Oryza sativa L.) consists of two major subspecies, indica and japonica. Inter-subspecific hybrids between indica and japonica, usually accompanying hybrid sterility, exhibit much more vigorous heterosis than intra-subspecific hybrids. f5 locus, also called S24 or Sb, confers significant effects on hybrid male sterility and segregation distortion. BC14F2 plants with f5-i/i, f5-j/j and f5-i/j genotype respectively, were used to dissect the underlying pathway of f5-caused hybrid male sterility via comparative transcriptome analysis. 350, 421, and 480 differentially expressed genes (DEGs) were identified from f5-i/j vs. f5-j/j, f5-j/j vs. f5-i/i, and f5-i/j vs. f5-i/i respectively. 145 DEGs demonstrated simultaneously differential expression in both f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i. Enrichment analysis with MapMan and AgriGO indicated that protein and DNA metabolism, and cell control related processes were enriched in the 145 DEGs. Stress and cell control related processes were enriched in the DEGs of f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i, whereas, these two processes were not enriched in the DEGs of f5-j/j vs. f5-i/i. Biotic and abiotic stress resistance genes were suppressed, which may result in pollen cell more sensitive to various stresses. The down regulation of ascorbate peroxidase (APX) may break the dynamic homeostasis of ROS (reactive oxygen species) and cause oxidative stress, which can damage cellular components. The expression of most of the heat shock protein (HSP) genes, which can protect proteins and cells from been destroyed, were also decreased. Based on these results, a model was proposed to summarize the underlying process for f5-caused rice hybrid male sterility. These results provide significant clues to further dissecting the molecular mechanism of f5-caused intersubspecific reproductive barrier.
2021-02-12 | GSE110483 | GEO
Project description:Contagious ecthyma (Orf) is a contagious disease with worldwide distribution, caused by the epitheliotropic Orf virus (ORFV), a member of the genus Parapoxvirus. In the current study, we collected the oral mucosa tissues samples (T0, T3, T7 and T15) from sheep at 0, 3, 7 and 15 days post ORFV infection, respectively. To explore the changes of comprehensive transcriptome of host cells from oral mucosa tissues post ORFV infection, the RNA-seq transcriptome comparisons were performed on these samples. It showed that 1928, 3219 and 2646 differentially expressed genes (DEGs) were identified among T3 vs. T0, T7 vs. T0, T15 vs. T0 respectively. Through Gene Ontology (GO) analyses of the DEGs from these comparisons, it revealed that ORFV provoked the vigorous immune response of the host cells during the early stage of infection. Moreover, GO and network analysis revealed that positive and negative regulative mechanisms of apoptosis worked as whole in the host cells, in order to reach a homeostasis of oral mucosa tissues.
2018-02-13 | GSE95203 | GEO
Project description:Heat stress (HS) could damage animal reproduction, while the mechanisms are still required to be better understood. Here, we showed that incubation of porcine immature Sertoli cells (iSCs) at 43 °C for 30 minutes followed 36h recovery under normal culture could inhibit the proliferation, promote apoptosis and increase the lactate production. Then, we profiled mRNA expression by RNA sequencing on Control (before HS), HS0.5 (0h after HS) and HS0.5-R36 (36h recovery after HS) groups of iSCs. We identified 126 (92 up- and 64 down-regulated), 3372 (2076 up- and 1296 down-regulated) and 3096 (1772 up- and 1324 down-regulated) differentially expressed (DE) mRNAs respectively in HS0 vs. Control, HS0-R36 vs. HS0 and HS0-R36 vs. Control comparisons. Gene ontology (GO ) enrichment found multiple significantly enriched biological pathways involved in different comparisons, including cellular response to heat, heat shock protein binding, regulation of cellular response to stress, RNA polyadenylation, sterol biosynthetic process, positive regulation of stress-activated MAPK cascade, chaperone-mediated protein folding, ATPase activity, cell cycle process and DNA replication etc. KEGG analysis showed the changed pathways, including cell cycle, MAPK, P53, PI3K-AKT, GnRH, HIF1, Wnt, cAMP signal pathways and Glycolysis/Gluconeogenesis etc. RT-qPCR validation of 9 DEGs (DNAJB1, TRAF6, INSIG1, GADD45G, HDAC6, FKBP4, SERPINE1, PFKP and GALM) showed the expression change trend of most DEGs (except TRAF6) consistent with the RNA-seq. Moreover, 6 of HSPs (HSPA6, HSPB1, HSPD1, HSP90AA1, HSP90AB1 and HSPH1) were validated by RT-qPCR and 5 of 6 (except HSP90AB1) showed the similar expression trend to RNA-seq results. Further validation of HSP90AA1 on protein level via immunostaining and westernbloting showed similar expression trend to RT-qPCR and RNA-seq. Taken together, HS could extensively change the global transcriptome, especially HSPs, to affect proliferation, apoptosis and metabolite production of pig iSCs.
2024-03-04 | GSE168427 | GEO
Project description:Analyzing changes in gene expression in liver and skeletal muscle from streptozotocin-diabetic rats. From the 9,929 expressed genes across the genome, 1,305 and 997 differentially expressed genes (DEGs, P < 0.01) were identified in comparisons of skeletal muscle and liver, respectively. Interestingly, large numbers of DEGs (200) were common to both comparisons, which was clearly more than the predicted number (131 genes, P < 10−4). Further interpretation of gene ontology used three over-representation analysis software (WebGestalt, Expander and GATHER). All the tools detected one KEGG pathway (MAPK signaling) and two GO biological processes (response to stress and cell death), with enrichment of DEGs in both tissues. In addition, PPI (protein-protein interaction) networks constructed using human homologs not only revealed the tendency of DEGs to form a highly connected module, but also suggested a “hub” role of MAPK related genes (such as MAPK14) in the pathogenesis of T2D. Total RNA obtained from liver and skeletal muscle of streptozotocin-diabetic rats and controls, respectivly.
2012-10-27 | E-GEOD-41832 | biostudies-arrayexpress
Project description:Common bean (Phaseolus vulgaris L.) is a relevant crop cultivated over the world, largely in water insufficiency vulnerable areas. Since drought is the main environmental factor restraining worldwide crop production, efforts have been invested to amend drought tolerance in commercial common bean varieties. However, scarce molecular data are available for those cultivars of P. vulgaris with drought tolerance attributes. As a first approach, Pinto Saltillo (PS), Azufrado Higuera (AH), and Negro Jamapa Plus (NP) were assessed phenotypically and physiologically to determine the outcome in response to drought on these common bean cultivars. Based on this, a Next-generation sequencing approach was applied to PS, which was the most drought-tolerant cultivar to determine the molecular changes at the transcriptional level. The RNA-Seq analysis revealed that numerous PS genes are dynamically modulated by drought. In brief, 1005 differentially expressed genes (DEGs) were identified, from which 645 genes were up-regulated by drought stress, whereas 360 genes were down-regulated. Further analysis showed that the enriched categories of the up-regulated genes in response to drought fit to processes related to carbohydrate metabolism (polysaccharide metabolic processes), particularly genes encoding proteins located within the cell periphery (cell wall dynamics). In the case of down-regulated genes, heat shock-responsive genes, mainly associated with protein folding, chloroplast, and oxidation-reduction processes were identified. Our findings suggest that secondary cell wall (SCW) properties contribute to P. vulgaris L. drought tolerance through alleviation or mitigation of drought-induced osmotic disturbances, making cultivars more adaptable to such stress. Altogether, the knowledge derived from this study is significant for a forthcoming understanding of the molecular mechanisms involved in drought tolerance on common bean, especially for drought-tolerant cultivars such as PS.
2019-12-31 | GSE123381 | GEO
Project description:To identify genes and metabolic pathways involved in the heat-stress response, digital gene expression analysis was performed on the midgut of thermotolerant silkworm variety ‘932’ and thermosensitive variety ‘HY’ after exposure to high temperature (932T and HYT). Deep sequencing yielded 6,211,484, 5,898,028, 5,870,395, and 6,088,303 reads for the 932, 932T, HY, and HYT samples, respectively. After filtering adaptor sequences and removing low-quality tags, 6,139,297, 5,828,615, 5,799,074, and 6,005,746 clean tags remained, respectively. The annotated genes associated with these tags numbered 4357, 4378, 4296, and 4658 for the 932, 932T, HY, and HYT samples, respectively. In HY-vs-932, 932-vs-932T, and HY-vs-HYT comparisons, 561, 316, and 281 differentially expressed genes were identified, which could be assigned to 179, 140, and 123 biological pathways, respectively.
2015-12-31 | GSE55990 | GEO