scholarly journals Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response to Drought Stress

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Chunsheng Gao ◽  
Chaohua Cheng ◽  
Lining Zhao ◽  
Yongting Yu ◽  
Qing Tang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Differentially Expressed Genes ◽  
Cannabis Sativa ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Signal Transduction Pathway ◽  
Differentially Expressed ◽  
Growth And Yield ◽  
Rna Seq ◽  
Kegg Pathways

Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9.83, 11.30, 11.66, and 11.31 M clean reads in the CK1, CK2, DS1, and DS2 libraries, respectively. A total of 1292 differentially expressed genes (DEGs), including 409 (31.66%) upregulated and 883 (68.34%) downregulated genes, were identified. The expression patterns of 12 selected genes were validated by qRT-PCR, and the results were accordant with Illumina analysis. Gene Ontology (GO) and KEGG analysis illuminated particular important biological processes and pathways, which enriched many candidate genes such as NAC, B3, peroxidase, expansin, and inositol oxygenase that may play important roles in hemp tolerance to drought. Eleven KEGG pathways were significantly influenced, the most influenced being the plant hormone signal transduction pathway with 15 differentially expressed genes. A similar expression pattern of genes involved in the abscisic acid (ABA) pathway under drought, and ABA induction, suggested that ABA is important in the drought stress response of hemp. These findings provide useful insights into the drought stress regulatory mechanism in hemp.

scholarly journals Comparative RNA-Seq analysis reveals genes associated with masculinization in female Cannabis sativa

Planta ◽  
2021 ◽  
Vol 253 (1) ◽  
Author(s):  
Ayelign M. Adal ◽  
Ketan Doshi ◽  
Larry Holbrook ◽  
Soheil S. Mahmoud
Keyword(s):  
Differentially Expressed Genes ◽  
Cannabis Sativa ◽  
Expression Patterns ◽  
Plant Biotechnology ◽  
Male Flower ◽  
Sex Expression ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Rna Profiling ◽  
Male Flowers

Abstract Main conclusion Using RNA profiling, we identified several silver thiosulfate-induced genes that potentially control the masculinization of female Cannabis sativa plants. Abstract Genetically female Cannabis sativa plants normally bear female flowers, but can develop male flowers in response to environmental and developmental cues. In an attempt to elucidate the molecular elements responsible for sex expression in C. sativa plants, we developed genetically female lines producing both female and chemically-induced male flowers. Furthermore, we carried out RNA-Seq assays aimed at identifying differentially expressed genes responsible for male flower development in female plants. The results revealed over 10,500 differentially expressed genes, of which around 200 potentially control masculinization of female cannabis plants. These genes include transcription factors and other genes involved in male organ (i.e., anther and pollen) development, as well as genes involved in phytohormone signalling and male-biased phenotypes. The expressions of 15 of these genes were further validated by qPCR assay confirming similar expression patterns to that of RNA-Seq data. These genes would be useful for understanding predisposed plants producing flowers of both sex types in the same plant, and help breeders to regulate the masculinization of female plants through targeted breeding and plant biotechnology.

scholarly journals Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Songbai Yang ◽  
Xiaolong Zhou ◽  
Yue Pei ◽  
Han Wang ◽  
Ke He ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Hormone Secretion ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
The Novel ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Single Organism

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P≤0.05, log2  Ratio≥1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

scholarly journals HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 244 ◽  
Author(s):  
Antonio Victor Campos Coelho ◽  
Rossella Gratton ◽  
João Paulo Britto de Melo ◽  
José Leandro Andrade-Santos ◽  
Rafael Lima Guimarães ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Differentially Expressed Genes ◽  
Cd4 T Cells ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Infected Cells ◽  
Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

scholarly journals Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 183 ◽  
Author(s):  
Oh ◽  
Lim ◽  
Song ◽  
Ahn ◽  
Lee ◽  
...  
Keyword(s):  
Varicella Zoster Virus ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Dermal Fibroblasts ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Human Dermal Fibroblasts ◽  
Varicella Zoster ◽  
Low Passage

Licensed live attenuated vaccines have been developed to prevent varicella zoster virus (VZV) infection, which causes chickenpox and shingles. The genomic sequences of both clinical- and vaccine-derived VZV strains have been analyzed previously. To further characterize the molecular signatures and complexity of wildtype (clinical) versus attenuated (vaccine-derived) VZV-mediated host cellular responses, we performed high-throughput next generation sequencing to quantify and compare the expression patterns of mRNAs and microRNAs (miRNAs) in primary human dermal fibroblasts (HDFs) infected with wildtype (YC01 low passage) and attenuated (YC01 high passage, SuduVax, and VarilRix) VZV strains. 3D-multidimensional scaling of the differentially expressed genes demonstrated the distinct grouping of wildtype and attenuated strains. In particular, we observed that HDFs infected with attenuated strains had more differentially expressed genes (DEGs) involved in the retinoic-acid inducible gene–I-like receptor and interferon-mediated signaling pathways compared with wildtype strains. Additionally, miRNA expression patterns were profiled following the infection of HDFs with VZV. Small RNA sequencing identified that several miRNAs were upregulated, including miR-146a-5p, which has been associated with other herpesvirus infections, whereas let-7a-3p was downregulated in both wildtype and attenuated VZV-infected cells. This study identified genes and miRNAs that may be essential in VZV pathogenesis.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Stress ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang , and node Ⅰ had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes ( OsIRT1 , OsNramp5, OsVIT2 , OsNRT1.5A, and OsABCC1 ) related to the “transporter activity” blocked the transport of Cd up to panicle and accumulation in grains of low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in “X”, but not in “y”, were all down-regulated by Cd stimulus. The up-regulation of miRNAs ( osa-miR528 and osa-miR408 ) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP , ERF , MYB , SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang . Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar . MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs , to play a role in stress response, which contribute to the response to Cd stress in rice.

RNA-seq analysis of non-muscular invasive bladder cancer to reveal different gene expression profiles between smoking and non-smoking patients.

2021 ◽  
Vol 39 (6_suppl) ◽  
pp. 478-478
Author(s):  
Zhichao Fu ◽  
Shenghua Liu ◽  
Jianfei Wang ◽  
Ning He ◽  
Yadong Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bladder Cancer ◽  
Tumor Progression ◽  
Urothelial Carcinoma ◽  
Differentially Expressed Genes ◽  
Poor Prognosis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Rna Seq

478 Background: Bladder cancer is the ninth most common malignancy in the world, approximately 75% of patients are diagnosed with non-muscle invasive bladder cancer (NMIBC). Smoking has been established to be a carcinogenic risk factor of bladder cancer. Nevertheless, the detailed relationship between smoking and progression of NMIBC are poorly understood. In this study, we revealed high expressed genes in smoking patients were significantly related to tumor progression in NMIBC patients. Methods: A total of 54 NMIBC patients including 19 never smokers and 35 smokers (current smokers and previous smokers) were enrolled in this study.The gene expression profiles were obtained by RNA-seq and the differentially expressed genes between smoking and non-smoking patients were identified using DESeq2 .The further analysis of the association between genes expression and patient survival in NMIBC cohorts(Jakob et al., 2016)and IMvigor 210 cohorts(Jonathan et al., 2016)by Kaplan-Meier survival estimate. Results: We identified 46 differentially expressed genes (p<0.05) in smoking and non-somking NMIBC patients. IDO1 and KRT14 gene, which related to bladder cancer progression and poor prognosis, was identified significantly higher expressed in somking group compared with non-smoking and they have a logFC of 2.6,3.9 with FDR 1.83E-5,3.40E-5 respectively. The expression of other genes, including KRT6A, CASP14, SERPINA1, MYO3A and IL20RB, were significantly higher in smoking patients compared to non-somking. Notably, survival data analysis from 476 NMIBC cohorts showed that IL20RB had a significant relationship with poor PFS(p = 0.021) and in the Mvigor 210 Cohort including 310 advanced or metastatic urothelial carcinoma patients treated with atezolizumab, we found that the high expression of IL20RB was significantly related to poor OS(p = 0.002). Conclusions: We identified 14 genes related to tumor progression were significantly higher in smoking NMIBC patients than in non-smoking. Among these genes, the expression of IL20RB was related to the poor prognosis of NMIBC, and it may correlates with reduced clinical benefit of immunotherapeutic in patients with urothelial carcinoma.

scholarly journals Transcriptomic analysis reveals distinct resistant response by physcion and chrysophanol against cucumber powdery mildew

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1991 ◽  
Author(s):  
Yanping Li ◽  
Shilin Tian ◽  
Xiaojun Yang ◽  
Xin Wang ◽  
Yuhai Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Disease Resistance ◽  
Powdery Mildew ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Defense Responses ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Sequencing Data ◽  
Transcriptional Change

Physcion and chrysophanol induce defense responses against powdery mildew in cucumbers. The combination of these two compounds has synergistic interaction against the disease. We performed RNA-seq on cucumber leaf samples treated with physcion and chrysophanol alone and with their combination. We generated 17.6 Gb of high-quality sequencing data (∼2 Gb per sample) and catalogued the expressions profiles of 12,293 annotated cucumber genes in each sample. We identified numerous differentially expressed genes that exhibited distinct expression patterns among the three treatments. The gene expression patterns of the Chr and Phy treatments were more similar to each other than to the Phy × Chr treatment. The Phy × Chr treatment induced the highest number of differentially expressed genes. This dramatic transcriptional change after Phy × Chr treatment leaves reflects that physcion combined with chrysophanol treatment was most closely associated with induction of disease resistance. The analysis showed that the combination treatment caused expression changes of numerous defense-related genes. These genes have known or potential roles in structural, chemical and signaling defense responses and were enriched in functional gene categories potentially responsible for cucumber resistance. These results clearly demonstrated that disease resistance in cucumber leaves was significantly influenced by the combined physcion and chrysophanol treatment. Thus, physcion and chrysophanol are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to the defense response.

scholarly journals Gene expression profiling of skeletal muscles

2021 ◽  
Author(s):  
Sarah I. Alto ◽  
Chih-Ning Chang ◽  
Kevin Brown ◽  
Chrissa Kioussi ◽  
Theresa M. Filtz
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Tibialis Anterior ◽  
Skeletal Muscles ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Analysis Tool

AbstractSoleus and tibialis anterior are two well-characterized skeletal muscles commonly utilized in skeletal muscle-related studies. Next-generation sequencing provides an opportunity for an in-depth biocomputational analysis to identify the gene expression patterns between soleus and tibialis anterior and analyze those genes’ functions based on past literature. This study acquired the gene expression profiles from soleus and tibialis anterior murine skeletal muscle biopsies via RNA-sequencing. Read counts were processed through edgeR’s differential gene expression analysis. Differentially expressed genes were filtered down using a false discovery rate less than 0.05c, a fold-change value larger than twenty, and an association with overrepresented pathways based on the Reactome pathway over-representation analysis tool. Most of the differentially expressed genes associated with soleus encoded for components of lipid metabolism and unique contractile elements. Differentially expressed genes associated with tibialis anterior encoded mostly for glucose and glycogen metabolic pathways’ regulatory enzymes and calcium-sensitive contractile components. These gene expression distinctions partly explain the genetic basis for muscle specialization and may help to explain skeletal muscle susceptibility to disease and drugs and refine tissue engineering approaches.

scholarly journals Multiomics Combined Analysis of Low-Phosphorus and Drought Stresses in Lotus Japonicus

2021 ◽  
Author(s):  
Ma Peijie+ ◽  
Li Yajiao+ ◽  
Shu Jianhong ◽  
Wang Ziyuan ◽  
Chen Xi ◽  
...  
Keyword(s):  
Drought Stress ◽  
Differentially Expressed Genes ◽  
Plant Hormone ◽  
Signal Transmission ◽  
Lotus Japonicus ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Kegg Pathways ◽  
Low Phosphorus ◽  
Transmission Pathways

Abstract BackgroundLotus japonicus is a perennial herb in Leguminosae. It is a good feed source and improves soil. It is also an excellent honey source and medicinal plant. Low-phosphorus and drought stresses are among the main abiotic stress factors limiting the production of pulse roots. MethodsIn this experiment, the effects of low-phosphorus and drought stresses on Baimai roots were analyzed under three treatments: control (zl1), low-phosphorus stress (zl2) and drought stress (zl3). Results A total of 2176, 3026 and 2980 differentially expressed genes were screened in zl1 vs. zl2, zl1 vs. zl3 and zl2 vs. zl3, respectively. The differentially expressed genes were enriched in functions related to cells, membranes, ion binding, enzyme activity and resistance to low-phosphorus and drought stresses. The enriched KEGG pathways included the MAPK signaling pathway-plant, flavor biosynthesis, starch and sucrose metabolism and plant hormone signal transmission. In particular, a large number of differentially expressed genes were enriched in the response to plant hormone signal transmission pathways among different treatments, and gene expression changes were analyzed. In addition, the differentially expressed genes identified under drought stress and the phase response genes identified under osmotic stress were upregulated. Differential metabolites were mainly enriched in the important metabolic pathways of flavonoid biosynthesis, arginine and proline metabolism and starch and sucrose metabolism. Differentially expressed proteins were mainly enriched in GO terms related to cell, membrane, ion binding and enzyme activity functions, and the main enriched KEGG pathways included the ribosome, starch and sucrose metabolism and plant hormone signal transmission pathways. ConclusionIn conclusion, these results of transcriptome, metabolome and proteome sequencing are helpful for understanding the response mechanisms, gene changes, metabolite changes and protein changes in Baimai roots under low-phosphorus and drought stress conditions to lay a foundation for future research on Lotus japonicus.

scholarly journals Insight of Transcriptional Regulators reveals the Tolerance Mechanism of Carpet-grass (Axonopus compressus) Against Drought

2021 ◽  
Author(s):  
Mohsin Nawaz ◽  
Liao Li ◽  
Farrukh Azeem ◽  
Samina Shabbir ◽  
Ali Zohaib ◽  
...  
Keyword(s):  
Drought Stress ◽  
Perennial Grass ◽  
Warm Season ◽  
Transcriptional Response ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Kegg Pathways ◽  
Public Data ◽  
Validation Experiment ◽  
Environmental Adaptations

Abstract Background: Carpet grass [Axonopus compressus (L.)] is an important warm-season perennial grass around the world and is known for its adaptability to varied environmental conditions. However, Carpet grass lacks enough data in public data banks, which confined our comprehension of the mechanisms of environmental adaptations, gene discovery, and development of molecular markers. In current study, the DEGs (differentially expressed genes) in Axonopus compressus under drought stress (DS) were identified and compared with CK (control) by RNA-Seq. Results: A total of 263,835 unigenes were identified in Axonopus compressus, and 201,303 (also added to the numbers of the remaining 2 databases) a sequence of unigenes significantly matched in at least one of the seven databases. A total of 153697 (58.25%) unigenes classified to 144 KEGG pathways, and 7,444 unigenes were expressed differentially between DS and CK, of which 4,249 were up-regulated and 3,195 were down-regulated unigenes. Of the 50 significantly enriched GO terms, 18, 6, and 14 items were related to BP, CC, and MF respectively. Analysis of KEGG enrichment revealed 2569 DEGs involved in 143 different pathways, under drought stress. 2,747 DEGs were up-regulated and 2,502 DEGs were down-regulated. Moreover, we identified 352 transcription factors (TFs) in Axonopus compressus, of which 270 were differentially expressed between CK and DS. The qRT-PCR validation experiment also supports the transcriptional response of Axonopus compressus against drought. Accuracy of transcriptome unigenes of Axonopus compressus was assessed with BLAST, which showed 3,300 sequences of Axonopus compressus in the NCBI.Conclusion: The 7,444 unigenes were found to be between DS and CK treatments, which indicate the existence of a strong mechanism of drought tolerance in Axonopus compressus. The current findings provide the first framework for further investigations for the particular roles of these unigenes in Axonopus compressus in response to drought.

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