scholarly journals Screening of Salt Stress Responsive Genes in Brachypodium distachyon (L.) Beauv. by Transcriptome Analysis

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1522
Author(s):  
Xiuxiu Guo ◽  
Qingjun Wang ◽  
Yuan Liu ◽  
Xuejie Zhang ◽  
Luoyan Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Transcriptome Analysis ◽  
Brachypodium Distachyon ◽  
Stomatal Closure ◽  
Differential Analysis ◽  
Oxygen Scavenging ◽  
Go Enrichment ◽  
Mapman Analysis ◽  
Upregulated Genes ◽  
Substance Metabolism

As one of the most common abiotic stresses, salt stress seriously impairs crop yield. Brachypodium distachyon (L.) Beauv. is a model species for studying wheat and other grasses. In the present investigation, the physiological responses of B. distachyon treated with different concentrations of NaCl for 24 h were measured. Therefore, the control and the seedlings of B. distachyon treated with 200 mM NaCl for 24 h were selected for transcriptome analysis. Transcriptome differential analysis showed that a total of 4116 differentially expressed genes (DEGs) were recognized, including 3120 upregulated and 996 downregulated ones. GO enrichment assay indicated that some subsets of genes related to the active oxygen scavenging system, osmoregulatory substance metabolism, and abscisic-acid (ABA)-induced stomatal closure were significantly upregulated under salt stress. The MapMan analysis revealed that the upregulated genes were dramatically enriched in wax metabolic pathways. The expressions of transcription factor (TF) family members such as MYB, bHLH, and AP2/ERF were increased under salt stress, regulating the response of plants to salt stress. Collectively, these findings provided valuable insights into the mechanisms underlying the responses of grass crops to salt stress.

Transcriptome analysis of a Triticum aestivum landrace (Roshan) in response to salt stress conditions

2021 ◽  
pp. 1-14
Author(s):  
Jamshid Azimian ◽  
Eslam Majidi Hervan ◽  
Amin Azadi ◽  
Mohammad Reza Bakhtiarizadeh ◽  
Reza Azizinezhad
Keyword(s):  
Salt Stress ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Meristem Maintenance ◽  
Polymerase Chain ◽  
Gene Expression Levels

Abstract In order to better understand the molecular mechanisms associated with salinity tolerance, transcriptome analysis of a local salt-tolerant wheat landrace (i.e. Roshan) was performed under salt stress. Transcriptome sequencing yielded 137,508,542 clean reads using the Illumina HiSeq 2000 platform. The results of two alignment programs, i.e. STAR and HISAT2, were used separately to perform the analysis of differentially expressed genes (DEGs) using DESeq2. Finally, a total of 17,897 DEGs were identified by DESeq2. Moreover, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses identified 108 GO terms and 62 significant KEGG pathways, of which ‘metabolic process’ and ‘metabolic pathways’ were the most abundant enriched term and pathway, respectively. Additionally, key salinity-tolerant genes, including asparagine synthetase, were also identified in the present study. Out of 87 identified families of transcription factors, GAI‐RGA ‐ and ‐SCR (GRAS) was one of the most important, which participates in signal transduction, and meristem maintenance and development. Eventually, to validate the gene expression levels, six DEGs were selected for a quantitative real-time polymerase chain reaction, and the results were in line with those of RNA-Seq. The findings of the current study can guide future genetic and molecular studies and allow a better understanding and improvement of salt tolerance in wheat.

Transcriptome analysis reveals genes potentially related to high fiber strength in a Gossypium hirsutum line IL9 with Gossypium mustelinum introgression

Genome ◽  
2021 ◽  
pp. 1-11
Author(s):  
Qi Chen ◽  
Wei Wang ◽  
Sameer Khanal ◽  
Jinlei Han ◽  
Mi Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Fiber Strength ◽  
Fiber Quality ◽  
Enrichment Analysis ◽  
Introgression Line ◽  
Recurrent Parent ◽  
High Fiber ◽  
Go Enrichment ◽  
Annotation Information ◽  
Cotton Fiber Quality

Cotton (Gossypium L.) is the most important fiber crop worldwide. Here, transcriptome analysis was conducted on developing fibers of a G. mustelinum introgression line, IL9, and its recurrent parent, PD94042, at 17 and 21 days post-anthesis (dpa). Differentially expressed genes (DEGs) of PD94042 and IL9 were identified. Gene Ontology (GO) enrichment analysis showed that the annotated DEGs were rich in two main biological processes and two main molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis likewise showed that the annotated DEGs were mainly enriched in metabolic pathways and biosynthesis of secondary metabolites. In total, 52 DEGs were selected as candidate genes based on comparison of the DEGs and GO function annotation information. Quantitative real-time PCR (RT-qPCR) analysis results for 12 randomly selected DEGs were consistent with transcriptome analysis. SNP identification based on G. mustelinum chromatin segment introgression showed that 394 SNPs were identified in 268 DEGs, and two genes with known functions were identified within fiber strength quantitative trait loci (QTL) regions or near the confidence intervals. We identified 52 key genes potentially related to high fiber strength in a G. mustelinum introgression line and provided significant insights into the study of cotton fiber quality improvement.

scholarly journals Transcriptomic Alterations Induced by Vemurafenib After Treatment of Melanoma: A Comprehensive Bioinformatics Analysis

2021 ◽  
Author(s):  
Jiaheng Xie ◽  
Yuan Cao ◽  
Zhechen Zhu ◽  
Shujie Ruan ◽  
Ming Wang ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Arrest ◽  
Enrichment Analysis ◽  
Skin Cell ◽  
Cycle Arrest ◽  
Go Enrichment ◽  
Cellular Sensitivity ◽  
Clinical Benefits ◽  
Melanoma Treatment ◽  
Upregulated Genes

Abstract Backgrounds Melanoma is a highly aggressive kind of cancer with very poor prognosis. B-raf inhibitor vemurafenib has indeed harvested substantial clinical benefits. Nevertheless, its drug resistance has also hampered scientists effort towards successful melanoma treatment. In this study, we used data derived from the GEO database to analyze the effect on vemurafenib sensitive cell lines after vemurafenib treatment. GEO datasets GSE42872 (cohort1), GSE127988 (cohort2), GSE110054 (cohort3) were included in the analysis. Results We found 25 common Differentially Expressed Genes(DEGs) in 3 datasets, including 10 upregulated genes and 15 downregulated genes after vemurefenib application. Analysis using web tool TIMER showed significant correlation of the upregulated genes with immune infiltration level in skin cell melanoma. GO enrichment analysis showed that after vemurafenib treatment, all datasets showed downregulation in DNA replication and cell cycle arrest. Meanwhile, genes related to neuro-generation, extracellular matrix and cell-cell adhesion were significantly enriched in all three datasets. KEGG analysis showed that pathways like P53, PI3K-Akt, and Rap signaling pathways were enriched in DEGs after vemurafenib administration.Conlusions The findings of the candidate DEGs and pathways may not only reveal the cellular sensitivity to vemurafenib treatment, but also give rise to a better understanding of the mechanism of cancer cell cycle arrest and cellular resistance towards vemurafenib targeted therapy.

Genotypic Characterization of Pseudomonas aeruginosa Isolates from Eyes with Keratitis and Healthy Conjunctival Sacs

2021 ◽  
Author(s):  
Xiubin Ma ◽  
Qing Liu ◽  
Fangying Song ◽  
Yusen Huang
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Group Versus ◽  
Therapeutic Interventions ◽  
Corneal Epithelial ◽  
Go Enrichment ◽  
Polymerase Chain ◽  
Upregulated Genes ◽  
Bacterial Secretion ◽  
Selection Of

Abstract Pseudomonas aeruginosa(P. aeruginosa) was a second most common commensal bacterium in healthy conjunctival sacs. When the corneal epithelial barrier is damaged, P. aeruginosa could cause keratitis, which progresses rapidly and results in corneal perforation and the loss of vision. However, the similarities and differences in characteristics between P. aeruginosa isolates from the eyes with keratitis and those from healthy conjunctival sacs are still poorly understood. In this study, four P. aeruginosa isolates from eyes with keratitis and three P. aeruginosa isolates from healthy conjunctival sacs were obtained, and genotypically characterized using Illumina high-throughput RNA sequencing. A total of 557 differentially expressed genes (DEGs) were found and included 332 upregulated genes and 225 downregulated genes in the keratitis group versus the healthy conjunctival sacs group. Of 557 DEGs, 11 DEGs analyzed with GO enrichment and the KEGG pathway were involved with the bacterial secretion system and pyoverdine metabolism and validated using quantitative reverse-transcription polymerase chain reaction. P. aeruginosa from eyes with keratitis induced more severe corneal infection and higher clinical scores in the mice. These results will contribute to develop alternative therapeutic interventions targeting virulence factors in these DEGs and facilitate the selection of therapeutic strategies.

Salt stress influence on stomatal and hydraulic conductivity, as well as on the level of aquaporins in leaf cells of barley plants, differing in salt tolerance

Biomics ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 280-287
Author(s):  
G.V. Sharipova ◽  
R.S. Ivanov ◽  
L.B. Vysotskaya ◽  
G.R. Akhiyarova
Keyword(s):  
Salt Stress ◽  
Hydraulic Conductivity ◽  
Stomatal Closure ◽  
Immunohistochemical Localization ◽  
Vascular Bundles ◽  
Salt Tolerant ◽  
Mesophyll Cells ◽  
Relationship Of ◽  
Concentration Assessment ◽  
Stress Influence

We studied participation of aquaporins in the regulation of leaf hydraulic conductivity and relationship of hydraulic conductivity with accumulation of ABA and stomatal closure during salt stress. Using the method of immunohistochemical localization we showed that salinity led to greater decline in the level of aquaporins in the region of the vascular leaf bundles of the more salt-tolerant Prairia cultivar, accompanied by a noticeable decrease in hydraulic conductivity of the leaf. In the less salt-tolerant plants of the Mikhailovsky cultivar, significant changes in the level of aquaporins under the influence of salt stress were not found. The degree of decrease in the hydraulic conductivity of the leaf in plants of two cultivars under the influence of salt stress correlated with a decrease in transpiration. Immunohistochemical localization of abscisic acid (ABA) in leaf cells showed that during salt stress this hormone accumulated in leaf mesophyll cells and stomata. The uptake of exogenous hormone from the nutrient solution and its entry into the leaf through the vascular bundles was accompanied by an increase in staining for aquaporins and the hydraulic conductivity of the leaves, which is characteristic of the ABA action. Differences in the localization of exogenous and endogenous hormones were obviously the cause of the opposite directions of changes in hydraulic conductivity: its increase under the influence of an exogenous ABA and a decrease - under the influence of salt stress. ABA concentration assessment in xylem showed the absence of its increase during salt stress, which explains the absence changes of staining for this hormone in the region of the leaf vascular bundles and indicates that accumulation of ABA in a short-term salt stress is not the result of its delivery from the roots, but the result of its synthesis in the shoot itself.

scholarly journals Identification of Salt Stress Responding Genes Using Transcriptome Analysis in Green Alga Chlamydomonas reinhardtii

2018 ◽  
Vol 19 (11) ◽  
pp. 3359 ◽  
Author(s):  
Ning Wang ◽  
Zhixin Qian ◽  
Manwei Luo ◽  
Shoujin Fan ◽  
Xuejie Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Chlamydomonas Reinhardtii ◽  
Green Alga ◽  
Transcriptome Analysis ◽  
Stress Responses ◽  
Electron Flow ◽  
Saline Stress ◽  
Alternative Source ◽  
Salt Stress Response ◽  
Stress Responding

Salinity is one of the most important abiotic stresses threatening plant growth and agricultural productivity worldwide. In green alga Chlamydomonas reinhardtii, physiological evidence indicates that saline stress increases intracellular peroxide levels and inhibits photosynthetic-electron flow. However, understanding the genetic underpinnings of salt-responding traits in plantae remains a daunting challenge. In this study, the transcriptome analysis of short-term acclimation to salt stress (200 mM NaCl for 24 h) was performed in C. reinhardtii. A total of 10,635 unigenes were identified as being differently expressed by RNA-seq, including 5920 up- and 4715 down-regulated unigenes. A series of molecular cues were screened for salt stress response, including maintaining the lipid homeostasis by regulating phosphatidic acid, acetate being used as an alternative source of energy for solving impairment of photosynthesis, and enhancement of glycolysis metabolism to decrease the carbohydrate accumulation in cells. Our results may help understand the molecular and genetic underpinnings of salt stress responses in green alga C. reinhardtii.

scholarly journals De novo transcriptome analysis of halotolerant bacterium Staphylococcus sp. strain P-TSB-70 isolated from East coast of India: In search of salt stress tolerant genes

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0228199 ◽  
Author(s):  
Priyanka Das ◽  
Bijay Kumar Behera ◽  
Soumendranath Chatterjee ◽  
Basanta Kumar Das ◽  
Trilochan Mohapatra
Keyword(s):  
Salt Stress ◽  
Transcriptome Analysis ◽  
East Coast ◽  
De Novo ◽  
De Novo Transcriptome ◽  
East Coast Of India ◽  
Halotolerant Bacterium

scholarly journals Transcriptome Analysis Reveals Significant Differences in Gene Expression of Malignant Pheochromocytoma or Paraganglioma

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Yong Joon Suh ◽  
Jung Ho Park ◽  
Sanchir-Erdene Bilegsaikhan ◽  
Dong Jin Lee
Keyword(s):  
Mrna Expression ◽  
Surgical Resection ◽  
Transcriptome Analysis ◽  
Clinical Information ◽  
The Cancer Genome Atlas ◽  
Eligibility Criteria ◽  
Mrna Expression Data ◽  
Cancer Genome Atlas ◽  
Tumeurs Endocrines ◽  
Upregulated Genes

Prediction of malignant behavior of pheochromocytoma (PC) or paraganglioma (PG) is of limited value. The Cancer Genome Atlas (TCGA) and the French ‘Cortico et Médullosurrénale: les Tumeurs Endocrines’ (COMETE) network in Paris (France) facilitate accurate differentiation of malignant PC/PG based on genetic information. Therefore, the objective of this transcriptome analysis is to identify the prognostic genes underlying the differentiation of malignant PC/PG in the TCGA and COMETE databases. TCGA carries data pertaining to multigenomic analysis of 173 PC/PG surgical resection samples while the COMETE cohort contains data involving 188 PC/PG surgical resection samples. Clinical information and mRNA expression datasets were downloaded from TCGA and COMETE databases. Based on eligibility criteria, 58 of 173 PC/PG samples in TCGA and 171 of 188 PC/PG samples collected by the COMETE network were selected. Using Ingenuity Pathway Analysis, the mRNA expression of malignant and benign PC/PG was compared. The 58 samples in TCGA included 11 malignant and 47 benign cases. Among the 171 samples obtained from the COMETE cohort, 19 were malignant and 152 were benign. A comparative analysis of the mRNA expression data of the two databases revealed that 11 up/downregulated pathways involved in malignant PC/PG were related to cancer signaling, metabolic alteration, and prominent mitosis, whereas 6 upregulated genes and 1 downregulated gene were significantly enriched in the functional annotation pathways. The TCGA and COMETE databases showed differences in mRNA expression associated with malignant and benign PC/PG. Improved recognition of prognostic genes facilitates the diagnosis and treatment of PC/PG.

scholarly journals Investigation of a Novel Salt Stress-Responsive Pathway Mediated by Arabidopsis DEAD-Box RNA Helicase Gene AtRH17 Using RNA-Seq Analysis

2020 ◽  
Vol 21 (5) ◽  
pp. 1595 ◽  
Author(s):  
Hye-Yeon Seok ◽  
Linh Vu Nguyen ◽  
Doai Van Nguyen ◽  
Sun-Young Lee ◽  
Yong-Hwan Moon
Keyword(s):  
Salt Stress ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Rna Helicase ◽  
Rna Seq ◽  
Salt Stress Tolerance ◽  
Salt Stress Condition ◽  
Dead Box ◽  
Helicase Gene ◽  
Upregulated Genes

Previously, we reported that overexpression of AtRH17, an Arabidopsis DEAD-box RNA helicase gene, confers salt stress-tolerance via a pathway other than the well-known salt stress-responsive pathways. To decipher the salt stress-responsive pathway in AtRH17-overexpressing transgenic plants (OXs), we performed RNA-Sequencing and identified 397 differentially expressed genes between wild type (WT) and AtRH17 OXs. Among them, 286 genes were upregulated and 111 genes were downregulated in AtRH17 OXs relative to WT. Gene ontology annotation enrichment and KEGG pathway analysis showed that the 397 upregulated and downregulated genes are involved in various biological functions including secretion, signaling, detoxification, metabolic pathways, catabolic pathways, and biosynthesis of secondary metabolites as well as in stress responses. Genevestigator analysis of the upregulated genes showed that nine genes, namely, LEA4-5, GSTF6, DIN2/BGLU30, TSPO, GSTF7, LEA18, HAI1, ABR, and LTI30, were upregulated in Arabidopsis under salt, osmotic, and drought stress conditions. In particular, the expression levels of LEA4-5, TSPO, and ABR were higher in AtRH17 OXs than in WT under salt stress condition. Taken together, our results suggest that a high AtRH17 expression confers salt stress-tolerance through a novel salt stress-responsive pathway involving nine genes, other than the well-known ABA-dependent and ABA-independent pathways.

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