scholarly journals Transcriptome Analysis of a Jujube (Ziziphus Jujuba Mill.) Cultivar Response to Heat Stress

2021 ◽  
Author(s):  
Lei Yang ◽  
Juan Jin ◽  
Ding-yu Fan ◽  
Qing Hao ◽  
Jianxin Niu
Keyword(s):  
Gene Ontology ◽  
Heat Stress ◽  
Stress Response ◽  
Heat Resistance ◽  
Molecular Mechanism ◽  
Cdna Libraries ◽  
Biological Processes ◽  
Rna Seq ◽  
Ziziphus Jujuba ◽  
Growth And Reproduction

Abstract Background: Heat stress (HS) is a common stress and influences the growth and reproduction of plant species. We found and bred a putative heat-resistant jujube (Ziziphus jujuba Mill.) cultivar (JHR17) in previous study. Results: In the current study, we made the seedlings of ‘JHR17’ cultivar to be under HS (45°C) for 0, 1, 3, 5 and 7 days, respectively, and the leaf samples (HR0, HR1, HR3, HR5 and HR7) were collected accordingly. Fifteen cDNA libraries from ‘JHR17’ leaves were built with a transcriptome assay. The RNA sequencing (RNA-seq) and transcriptome comparisons were performed, and the results indicated that 1642, 4080, 5160 and 2119 differentially expressed genes (DEGs) were identified in HR1 vs. HR0, HR3 vs. HR0, HR5 vs. HR0 and HR7 vs. HR0, respectively. Gene Ontology (GO) analyses of the DEGs from these comparisons were implemented. Conclusion: It revealed that a series of biological processes, involved in stress response, photosynthesis and metabolism, were enriched successfully, suggesting that lowering or up-regulating these genes of processes might play important roles in response to HS. This study may contribute to understand the molecular mechanism of ‘JHR17’ cultivar response to HS, and be beneficial for developing jujube cultivars to improve heat resistance.

scholarly journals Transcriptome Analysis of Jujube (Ziziphus jujuba Mill.) Response to Heat Stress

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Lei Yang ◽  
Juan Jin ◽  
Dingyu Fan ◽  
Qing Hao ◽  
Jianxin Niu
Keyword(s):  
Gene Ontology ◽  
Heat Stress ◽  
Abiotic Stress ◽  
Molecular Mechanism ◽  
Stress Responses ◽  
Stress Resistance ◽  
Cdna Libraries ◽  
Biological Processes ◽  
Ziziphus Jujuba ◽  
Growth And Reproduction

Heat stress (HS) is a common stress influencing the growth and reproduction of plant species. Jujube (Ziziphus jujuba Mill.) is an economically important tree with strong abiotic stress resistance, but the molecular mechanism of its response to HS remains elusive. In this study, we subjected seedlings of Z. jujuba cultivar “Hqing1-HR” to HS (45°C) for 0, 1, 3, 5, and 7 days, respectively, and collected the leaf samples (HR0, HR1, HR3, HR5, and HR7) accordingly. Fifteen cDNA libraries from leaves were constructed for transcriptomics assays. RNA sequencing and transcriptomics identified 1,642, 4,080, 5,160, and 2,119 differentially expressed genes (DEGs) in comparisons of HR1 vs. HR0, HR3 vs. HR0, HR5 vs. HR0, and HR7 vs. HR0, respectively. Gene ontology analyses of the DEGs from these comparisons revealed enrichment in a series of biological processes involved in stress responses, photosynthesis, and metabolism, suggesting that lowering or upregulating expression of these genes might play important roles in the response to HS. This study contributed to our understanding of the molecular mechanism of jujube response to HS and will be beneficial for developing jujube cultivars with improved heat resistance.

RNA-Seq-mediated transcriptomic analysis of heat stress response in a polar Chlorella sp. (Trebouxiophyceae, Chlorophyta)

2018 ◽  
Vol 30 (6) ◽  
pp. 3103-3119 ◽  
Author(s):  
Sze-Wan Poong ◽  
Kok-Keong Lee ◽  
Phaik-Eem Lim ◽  
Tun-Wen Pai ◽  
Chiew-Yen Wong ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Transcriptomic Analysis ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Chlorella Sp

scholarly journals The Molecular Mechanism of Multiple Organ Dysfunction and Targeted Intervention of COVID-19 Based on Time-Order Transcriptomic Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Miao Zou ◽  
Xiaoyun Su ◽  
Luoying Wang ◽  
Xingcheng Yi ◽  
Yue Qiu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stress Response ◽  
Molecular Mechanism ◽  
Organ Dysfunction ◽  
Multiple Organ ◽  
Biological Processes ◽  
Cytokine Storm ◽  
Multiple Organ Dysfunction ◽  
Hub Genes ◽  
Immune Genes

Coronavirus disease 2019 (COVID-19) pandemic is caused by the novel coronavirus that has spread rapidly around the world, leading to high mortality because of multiple organ dysfunction; however, its underlying molecular mechanism is unknown. To determine the molecular mechanism of multiple organ dysfunction, a bioinformatics analysis method based on a time-order gene co-expression network (TO-GCN) was performed. First, gene expression profiles were downloaded from the gene expression omnibus database (GSE161200), and a TO-GCN was constructed using the breadth-first search (BFS) algorithm to infer the pattern of changes in the different organs over time. Second, Gene Ontology enrichment analysis was used to analyze the main biological processes related to COVID-19. The initial gene modules for the immune response of different organs were defined as the research object. The STRING database was used to construct a protein–protein interaction network of immune genes in different organs. The PageRank algorithm was used to identify five hub genes in each organ. Finally, the Comparative Toxicogenomics Database played an important role in exploring the potential compounds that target the hub genes. The results showed that there were two types of biological processes: the body’s stress response and cell-mediated immune response involving the lung, trachea, and olfactory bulb (olf) after being infected by COVID-19. However, a unique biological process related to the stress response is the regulation of neuronal signals in the brain. The stress response was heterogeneous among different organs. In the lung, the regulation of DNA morphology, angiogenesis, and mitochondrial-related energy metabolism are specific biological processes related to the stress response. In particular, an effect on tracheal stress response was made by the regulation of protein metabolism and rRNA metabolism-related biological processes, as biological processes. In the olf, the distinctive stress responses consist of neural signal transmission and brain behavior. In addition, myeloid leukocyte activation and myeloid leukocyte-mediated immunity in response to COVID-19 can lead to a cytokine storm. Immune genes such as SRC, RHOA, CD40LG, CSF1, TNFRSF1A, FCER1G, ICAM1, LAT, LCN2, PLAU, CXCL10, ICAM1, CD40, IRF7, and B2M were predicted to be the hub genes in the cytokine storm. Furthermore, we inferred that resveratrol, acetaminophen, dexamethasone, estradiol, statins, curcumin, and other compounds are potential target drugs in the treatment of COVID-19.

scholarly journals Comprehensive RNA-Seq Profiling Reveals Temporal and Tissue-Specific Changes in Gene Expression in Sprague–Dawley Rats as Response to Heat Stress Challenges

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinhuan Dou ◽  
Angela Cánovas ◽  
Luiz F. Brito ◽  
Ying Yu ◽  
Flavio S. Schenkel ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Metabolic Pathways ◽  
Adrenal Glands ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Mammal Species ◽  
Heat Stress Response ◽  
Sprague Dawley Rats

Understanding heat stress physiology and identifying reliable biomarkers are paramount for developing effective management and mitigation strategies. However, little is known about the molecular mechanisms underlying thermal tolerance in animals. In an experimental model of Sprague–Dawley rats subjected to temperatures of 22 ± 1°C (control group; CT) and 42°C for 30 min (H30), 60 min (H60), and 120 min (H120), RNA-sequencing (RNA-Seq) assays were performed for blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120). A total of 53, 1,310, and 1,501 differentially expressed genes (DEGs) were significantly identified in the blood (P < 0.05 and |fold change (FC)| >2), liver (P < 0.01, false discovery rate (FDR)–adjusted P = 0.05 and |FC| >2) and adrenal glands (P < 0.01, FDR-adjusted P = 0.05 and |FC| >2), respectively. Of these, four DEGs, namely Junb, P4ha1, Chordc1, and RT1-Bb, were shared among the three tissues in CT vs. H120 comparison. Functional enrichment analyses of the DEGs identified in the blood (CT vs. H120) revealed 12 biological processes (BPs) and 25 metabolic pathways significantly enriched (FDR = 0.05). In the liver, 133 BPs and three metabolic pathways were significantly detected by comparing CT vs. H30, H60, and H120. Furthermore, 237 BPs were significantly (FDR = 0.05) enriched in the adrenal glands, and no shared metabolic pathways were detected among the different heat-stressed groups of rats. Five and four expression patterns (P < 0.05) were uncovered by 73 and 91 shared DEGs in the liver and adrenal glands, respectively, over the different comparisons. Among these, 69 and 73 genes, respectively, were proposed as candidates for regulating heat stress response in rats. Finally, together with genome-wide association study (GWAS) results in cattle and phenome-wide association studies (PheWAS) analysis in humans, five genes (Slco1b2, Clu, Arntl, Fads1, and Npas2) were considered as being associated with heat stress response across mammal species. The datasets and findings of this study will contribute to a better understanding of heat stress response in mammals and to the development of effective approaches to mitigate heat stress response in livestock through breeding.

scholarly journals Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across different sites

2020 ◽  
Author(s):  
Anish M.S. Shrestha ◽  
Crissa Ann I. Lilagan ◽  
Joyce Emlyn B. Guiao ◽  
Maria Rowena R. Romana-Eguia ◽  
Ma. Carmen Ablan Lagman
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
The Philippines ◽  
Differentially Expressed ◽  
Scylla Serrata ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Site Analysis ◽  
Mangrove Crab ◽  
Heat Response

Abstract Background: The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab seeds from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response.Results: We present the first ever transcriptome assembly of S. serrata obtained from a massive data set containing ~66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Based on sequence comparison to the fruitfly and shrimp proteomes, our assembly contains several thousands of almost full-length transcripts. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis of difference in heat response showed that between Cagayan and Bataan, there were 389 differently differentially expressed (DDE) genes associated with 48 signalling and stress-response pathways; and between Cagayan and Bicol, there were 101 DDE genes affecting 8 pathways.Conclusion: In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

scholarly journals The muscle development transcriptome landscape of ovariectomized goat

2017 ◽  
Vol 4 (12) ◽  
pp. 171415 ◽  
Author(s):  
Sihuan Zhang ◽  
Han Xu ◽  
Xinfeng Liu ◽  
Qing Yang ◽  
Chuanying Pan ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Muscle Development ◽  
Enrichment Analysis ◽  
Repeat Sequence ◽  
Cdna Libraries ◽  
Polymorphism Analysis ◽  
Rna Seq ◽  
Single Nucleotide ◽  
Almost All ◽  
Go Terms

In practical production, almost all rams and about 50% of ewes are used to fatten. Researchers have proved that ewe ovariectomy could improve the productivity significantly, but the specific molecular mechanism is still unknown. In this study, five independent cDNA libraries (three and two from ovariectomized and normal ewe longissimus dorsi samples, respectively) were constructed to thoroughly explore the global transcriptome, further to reveal how the ovariectomized ewes influence muscle development by Illumina2000 sequencing technology. As a result, 205 358 transcripts and 118 264 unigenes were generated. 15 490 simple sequence repeats (SSRs) were revealed and divided into six types, and the short repeat sequence SSR (monomers, dimers, trimers) was the domain type. Single nucleotide polymorphism analysis found that the number of transition was greater than the number of transversion among the five libraries. Furthermore, 1612 differently expressed genes (DEGs) (Log2fold_change > 1 and p  < 0.05) were revealed between ovariectomized and normal ewe groups, in which 903 genes were expressed commonly in the two groups, and 288 and 421 genes were uniquely expressed in normal and ovariectomized ewe groups, respectively. Gene Ontology (GO) analysis categorized all unigenes into 555 GO terms and 56 DEGs were significantly categorized into 43 GO terms ( p  < 0.05). KEGG enrichment analysis annotated 12 976 genes (containing 137 DEGs) to 86 pathways, among them 24 and 11 DEGs involved in development and reproduction associated pathways, respectively. To validate the reliability of the RNA-seq analysis, 22 candidate DEGs were randomly selected to perform quantitative real-time polymerase chain reaction. The result showed that 9 and 1 genes were significantly and approximately significantly expressed in control and treatment group, respectively, and the results of RNA-seq are believable in this study. Overall, these results were helpful for elucidating the molecular mechanism of muscle development of ovariectomized animals and the application of female ovariectomy in fattening.

scholarly journals Liver Transcriptome Changes of Hyla Rabbit in Response to Chronic Heat Stress

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1141
Author(s):  
Zhou-Lin Wu ◽  
Xue Yang ◽  
Shi-Yi Chen ◽  
Fei-Long Deng ◽  
Xian-Bo Jia ◽  
...  
Keyword(s):  
Heat Stress ◽  
Metabolic Process ◽  
Pcr Analysis ◽  
P Value ◽  
Biological Processes ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Liver Transcriptome ◽  
Quality Filtering ◽  
Gene Expression Levels

Rabbit is an economically important farm animal in China and also is a widely used animal model in biological researches. Rabbits are very sensitive to the environmental conditions, therefore we investigated the liver transcriptome changes in response to chronic heat stress in the present study. Six Hyla rabbits were randomly divided into two groups: chronic heat stress (HS) and controls without heat stress (CN). Six RNA-Seq libraries totally yielded 380 million clean reads after the quality filtering. Approximately 85.07% of reads were mapped to the reference genome. After assembling transcripts and quantifying gene expression levels, we detected 51 differentially expressed genes (DEGs) between HS and CN groups with thresholds of the adjusted p-value < 0.05 and |log2(FoldChange)| > 1. Among them, 33 and 18 genes were upregulated and downregulated, respectively. Gene ontology analyses further revealed that these DEGs were mainly associated with metabolism of lipids, thyroid hormone metabolic process, and cellular modified amino acid catabolic process. The upregulated ACACB, ACLY, LSS, and CYP7A1 genes were found to be inter-related through biological processes of thioester biosynthetic process, acyl-CoA biosynthetic process, acetyl-CoA metabolic process, and others. Six DEGs were further validated by quantitative real-time PCR analysis. The results revealed the candidate genes and biological processes that will potentially be considered as important regulatory factors involved in the heat stress response in rabbits.

scholarly journals Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across sites of varying climate profiles

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anish M.S. Shrestha ◽  
Crissa Ann I. Lilagan ◽  
Joyce Emlyn B. Guiao ◽  
Maria Rowena R. Romana-Eguia ◽  
Ma. Carmen Ablan Lagman
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Transcriptome Assembly ◽  
The Philippines ◽  
Scylla Serrata ◽  
Rna Seq ◽  
Data Set ◽  
Heat Stress Response ◽  
Site Analysis ◽  
Mangrove Crab

Abstract Background The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab juveniles from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response. Results We present the first ever transcriptome assembly of S. serrata obtained from a data set containing 66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Our assembly contains many almost full-length transcripts – 5229 shrimp and 3049 fruit fly proteins have alignments that cover >80% of their sequence lengths to a contig. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat-stress response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis showed that between Cagayan and Bataan, there were 389 genes associated with 48 signaling and stress-response pathways, for which there was an effect of site in the response to heat; and between Cagayan and Bicol, there were 101 such genes affecting 8 pathways. Conclusion In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

scholarly journals Heat Stress-Responsive Transcriptome Analysis in the Liver Tissue of Hu Sheep

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 395 ◽  
Author(s):  
Yaokun Li ◽  
Lingxuan Kong ◽  
Ming Deng ◽  
Zhiquan Lian ◽  
Yinru Han ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Mechanism ◽  
Stress Responses ◽  
Animal Health ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Ppar Signaling ◽  
Hu Sheep

Heat stress has a severe effect on animal health and can reduce the productivity and reproductive efficiency; it is therefore necessary to explore the molecular mechanism involved in heat stress response, which is helpful for the cultivation of an animal breed with resistance to heat stress. However, little research about heat stress-responsive molecular analysis has been reported in sheep. Therefore, in this study, RNA sequencing (RNA-Seq) was used to investigate the transcriptome profiling in the liver of Hu sheep with and without heat stress. In total, we detected 520 and 22 differentially expressed mRNAs and lncRNAs, respectively. The differentially expressed mRNAs were mainly associated with metabolic processes, the regulation of biosynthetic processes, and the regulation of glucocorticoid; additionally, they were significantly enriched in the heat stress related pathways, including the carbon metabolism, the PPAR signaling pathway, and vitamin digestion and absorption. The co-located differentially expressed lncRNA Lnc_001782 might positively influence the expression of the corresponding genes APOA4 and APOA5, exerting co-regulative effects on the liver function. Thus, we made the hypothesis that Lnc_001782, APOA4 and APOA5 might function synergistically to regulate the anti-heat stress ability in Hu sheep. This study provides a catalog of Hu sheep liver mRNAs and lncRNAs, and will contribute to a better understanding of the molecular mechanism underlying heat stress responses.

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