scholarly journals Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 466 ◽  
Author(s):  
Erick Amombo ◽  
Xiaoning Li ◽  
Guangyang Wang ◽  
Shao An ◽  
Wei Wang ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Dna Sequences ◽  
Tall Fescue ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Interaction Analysis ◽  
Quantitative Polymerase Chain Reaction ◽  
Future Research ◽  
Salt Treatment ◽  
Gene Expressions

Soil salinity is a serious threat to plant growth and crop productivity. Tall fescue utilization in saline areas is limited by its inferior salt tolerance. Thus, a transcriptome study is a prerequisite for future research aimed at providing deeper insights into the molecular mechanisms of tall fescue salt tolerance as well as molecular breeding. Recent advances in sequencing technology offer a platform to achieve this. Here, Illumina RNA sequencing of tall fescue leaves generated a total of 144,339 raw reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to various databases. Further structural analyses revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. In total, 1862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs. 24 h salt treatment. Protein interaction analysis revealed a high interaction of chaperonins and Rubisco proteins in 48 h vs. 24 h salt treatment. The gene expressions were finally validated using quantitative polymerase chain reaction (qPCR), which was coherent with sequencing results.

Evaluation of Appropriate Reference Genes For Investigating Gene Expression in Chlorops oryzae (Diptera: Chloropidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2207-2214 ◽  
Author(s):  
Ping Tian ◽  
Lin Qiu ◽  
Ailin Zhou ◽  
Guo Chen ◽  
Hualiang He ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ribosomal Protein ◽  
Reference Genes ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Quantitative Polymerase Chain Reaction ◽  
Housekeeping Genes ◽  
Future Research ◽  
Economic Damage ◽  
Physiological Processes

Abstract Reverse transcription quantitative polymerase chain reaction (PCR) has become an invaluable technique for analyzing gene expression in many insects. However, this approach requires the use of stable reference genes to normalize the data. Chlorops oryzae causes significant economic damage to rice crops throughout Asia. The lack of suitable reference genes has hindered research on the molecular mechanisms underlying many physiological processes of this species. In this study, we used quantitative real-time PCR to evaluate the expression of eight C. oryzae housekeeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-actin (βACT), beta-tubulin (βTUB), Delta Elongation factor-1 (EF1δ), ribosomal protein S11 (RPS11), RPS15, C-terminal-Binding Protein (CtBP), and ribosomal protein 49 (RP49) in different developmental stages and tissues in both larvae and adults. We analyzed the data with four different software packages: geNorm, NormFinder, BestKeeper, and RefFinder and compared the results obtained with each method. The results indicate that PRS15 and RP49 can be used as stable reference genes for quantifying gene expression in different developmental stages and larval tissues. GAPDH and βACT, which have been considered stable reference genes by previous studies, were the least stable of the candidate genes with respect to larval tissues. GAPDH was, however, the most stable reference gene for adult tissues. We verified the candidate reference genes identified and found that the expression levels of Cadherins (Cads) changed when different reference genes were used to normalize gene expression. This study provides a valuable foundation for future research on gene function, and investigating the molecular basis of physiological processes, in C. oryzae.

scholarly journals The key regulator LcERF056 enhances salt tolerance by modulating reactive oxygen species-related genes in Lotus corniculatus

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dan Wang ◽  
Zhanmin Sun ◽  
Xinxu Hu ◽  
Junbo Xiong ◽  
Lizhen Hu ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Salt Tolerance ◽  
Lipid Transfer Protein ◽  
Quantitative Polymerase Chain Reaction ◽  
Reactive Oxygen ◽  
Lotus Corniculatus ◽  
Ethylene Response Factor ◽  
Oxygen Species ◽  
Lipid Transfer ◽  
Salt Treatment

Abstract Background The APETALA2/ethylene response factor (AP2/ERF) family are important regulatory factors involved in plants’ response to environmental stimuli. However, their roles in salt tolerance in Lotus corniculatus remain unclear. Results Here, the key salt-responsive transcription factor LcERF056 was cloned and characterised. LcERF056 belonging to the B3–1 (IX) subfamily of ERFs was considerably upregulated by salt treatment. LcERF056-fused GFP was exclusively localised to nuclei. Furthermore, LcERF056- overexpression (OE) transgenic Arabidopsis and L. corniculatus lines exhibited significantly high tolerance to salt treatment compared with wild-type (WT) or RNA interference expression (RNAi) transgenic lines at the phenotypic and physiological levels. Transcriptome analysis of OE, RNAi, and WT lines showed that LcERF056 regulated the downstream genes involved in several metabolic pathways. Chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR) and yeast one-hybrid (Y1H) assay demonstrated that LcERF056 could bind to cis-element GCC box or DRE of reactive oxygen species (ROS)-related genes such as lipid-transfer protein, peroxidase and ribosomal protein. Conclusion Our results suggested that the key regulator LcERF056 plays important roles in salt tolerance in L. corniculatus by modulating ROS-related genes. Therefore, it may be a useful target for engineering salt-tolerant L. corniculatus or other crops.

scholarly journals De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5681 ◽  
Author(s):  
Li Li ◽  
Mimi Li ◽  
Xiwu Qi ◽  
Xingli Tang ◽  
Yifeng Zhou
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Rna Sequencing ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Biosynthetic Pathways ◽  
Salt Stress Response ◽  
Glehnia Littoralis ◽  
Plant Signal Transduction

Soil salinity is one of the major environmental stresses affecting plant growth, development, and reproduction. Salt stress also affects the accumulation of some secondary metabolites in plants. Glehnia littoralis is an endangered medicinal halophyte that grows in coastal habitats. Peeled and dried Glehnia littoralis roots, named Radix Glehniae, have been used traditionally as a Chinese herbal medicine. Although Glehnia littoralis has great ecological and commercial value, salt-related mechanisms in Glehnia littoralis remain largely unknown. In this study, we analysed the transcriptome of Glehnia littoralis in response to salt stress by RNA-sequencing to identify potential salt tolerance gene networks. After de novo assembly, we obtained 105,875 unigenes, of which 75,559 were annotated in public databases. We identified 10,335 differentially expressed genes (DEGs; false discovery rate <0.05 and |log2 fold-change| ≥ 1) between NaCl treatment (GL2) and control (GL1), with 5,018 upregulated and 5,317 downregulated DEGs. To further this investigation, we performed Gene Ontology (GO) analysis and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DEGs involved in secondary metabolite biosynthetic pathways, plant signal transduction pathways, and transcription factors in response to salt stress were analysed. In addition, we tested the gene expression of 15 unigenes by quantitative real-time PCR (qRT-PCR) to confirm the RNA-sequencing results. Our findings represent a large-scale assessment of the Glehnia littoralis gene resource, and provide useful information for exploring its molecular mechanisms of salt tolerance. Moreover, genes enriched in metabolic pathways could be used to investigate potential biosynthetic pathways of active compounds by Glehnia littoralis.

scholarly journals Transcriptomic basis for salt tolerance and disease resistance of silverleaf sunflower revealed by Iso-seq and RNA-seq

2019 ◽  
Author(s):  
Jing Bing ◽  
Yunhe Ling ◽  
Peipei An ◽  
Enshi Xiao ◽  
Chunlian Li ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Salt Tolerance ◽  
Reference Genome ◽  
Transcriptome Assembly ◽  
Future Research ◽  
Rna Seq ◽  
Gene Expressions ◽  
Breeding Programs ◽  
Genomic Variance ◽  
Cultivated Species

Abstract Background Silverleaf sunflower, Helianthus argophyllus , is one of the most important wild species that have been usually used for the improvement of cultivated sunflower. Although a reference genome is now available for the cultivated species, H. annuus , its effect in helping understanding the mechanisms underlying the traits of H. argophyllus is limited by the substantial genomic variance between these two species.Results In this study, we generated a high-quality reference transcriptome of H. argophyllus using Iso-seq strategy. This assembly contains 50,153 unique genes covering more than 91% of the whole genes. Among them, we find 205 genes that are absent in the cultivated species and 475 fusion genes containing components of coding or non-coding sequences from the genome of H. annuus . It is interesting that in line with the strong disease resistance observed for H. argophyllus , these H. argophyllus -specific genes are predominantly related to functions of resistance. We have also profiled the gene expressions in leaf and root under normal or salt stressed conditions and, as a result, find distinct transcriptomic responses to salt stress in leaf and root. Particularly, genes involved in several critical processes including the synthesis and metabolism of glutamate and carbohydrate transport are reversely regulated in leaf and root.Conclusions Overall, this study provided insights into the genomic mechanisms underlying the disease resistance and salt tolerance of silverleaf sunflower and the transcriptome assembly and the genes identified in this study can serve as a complement data resources for future research and breeding programs of sunflowers.

scholarly journals Promising novel biomarkers and candidate small-molecule drugs for lung adenocarcinoma: Evidence from bioinformatics analysis of high-throughput data

Open Medicine ◽  
2021 ◽  
Vol 17 (1) ◽  
pp. 96-112
Author(s):  
Chengrui Li ◽  
Yufeng Wan ◽  
Weijun Deng ◽  
Fan Fei ◽  
Linlin Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Adenocarcinoma ◽  
Small Molecules ◽  
Molecular Mechanisms ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Expression Omnibus ◽  
Functional Enrichment ◽  
Receptor Interaction ◽  
Hub Genes ◽  
Gene Expressions

Abstract Lung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer associated with an unstable prognosis. Thus, there is an urgent demand for the identification of novel diagnostic and prognostic biomarkers as well as targeted drugs for LUAD. The present study aimed to identify potential new biomarkers associated with the pathogenesis and prognosis of LUAD. Three microarray datasets (GSE10072, GSE31210, and GSE40791) from the Gene Expression Omnibus database were integrated to identify the differentially expressed genes (DEGs) in normal and LUAD samples using the limma package. Bioinformatics tools were used to perform functional and signaling pathway enrichment analyses for the DEGs. The expression and prognostic values of the hub genes were further evaluated by Gene Expression Profiling Interactive Analysis and real-time quantitative polymerase chain reaction. Furthermore, we mined the “Connectivity Map” (CMap) to explore candidate small molecules that can reverse the tumoral of LUAD based on the DEGs. A total of 505 DEGs were identified, which included 337 downregulated and 168 upregulated genes. The PPI network was established with 1,860 interactions and 373 nodes. The most significant pathway and functional enrichment associated with the genes were cell adhesion and extracellular matrix-receptor interaction, respectively. Seven DEGs with high connectivity degrees (ZWINT, RRM2, NDC80, KIF4A, CEP55, CENPU, and CENPF) that were significantly associated with worse survival were chosen as hub genes. Lastly, top 20 most important small molecules which reverses the LUAD gene expressions were identified. The findings contribute to revealing the molecular mechanisms of the initiation and progression of LUAD and provide new insights for integrating multiple biomarkers in clinical practice.

Changes in Transcriptome and Gene Expression in Sogatella furcifera (Hemiptera: Delphacidae) in Response to Cycloxaprid

2020 ◽  
Author(s):  
Jian-Xue Jin ◽  
Zhao-Chun Ye ◽  
Dao-Chao Jin ◽  
Feng-Liang Li ◽  
Wen-Hong Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Virus Transmission ◽  
Resistance Mechanisms ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Sogatella Furcifera ◽  
Neonicotinoid Insecticide

Abstract The white-backed planthopper, Sogatella furcifera (Horváth), causes substantial damage to crops by direct feeding or virus transmission, especially southern rice black-streaked dwarf virus, which poses a serious threat to rice production. Cycloxaprid, a novel cis-nitromethylene neonicotinoid insecticide, has high efficacy against rice planthoppers, including imidacloprid-resistant populations. However, information about the influence of cycloxaprid on S. furcifera (Hemiptera: Delphacidae) at the molecular level is limited. Here, by de novo transcriptome sequencing and assembly, we constructed two transcriptomes of S. furcifera and profiled the changes in gene expression in response to cycloxaprid at the transcription level. We identified 157,906,456 nucleotides and 131,601 unigenes using the Illumina technology from cycloxaprid-treated and untreated S. furcifera. In total, 38,534 unigenes matched known proteins in at least one database, accounting for 29.28% of the total unigenes. The number of coding DNA sequences was 28,546 and that of amino acid sequences in the coding region was 22,299. In total, 15,868 simple sequence repeats (SSRs) were identified. The trinucleotide repeats accounted for 45.1% (7,157) of the total SSRs and (AAG/CTT)n were the most frequent motif. There were 359 differentially expressed genes that might have been induced by cycloxaprid. There were 131 upregulated and 228 downregulated genes. Twenty-two unigenes might be involved in resistance against cycloxaprid, such as cytochrome P450, glutathione S-transferase (GST), acid phosphatase (ACP), and cadherin. Our study provides vital information on cycloxaprid-induced resistance mechanisms, which will be useful to analyze the molecular mechanisms of cycloxaprid resistance and may lead to the development of novel strategies to manage S. furcifera.

scholarly journals The globe transcriptome analysis reveals hybrid effects and regulatory divergence between (Acanthopagrus schlegelii ♂× Pagrus major ♀) hybrid F1 and parents

2019 ◽  
Author(s):  
Shuyin Chen ◽  
Zhiyong Zhang ◽  
Hongjiu Ji ◽  
Shixia Xu ◽  
Yunxia Yang ◽  
...  
Keyword(s):  
Rapid Growth ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Whole Body ◽  
Hybridization Technique ◽  
Pagrus Major ◽  
Gene Expressions ◽  
Commercial Fish ◽  
Acanthopagrus Schlegelii

Abstract Background: Hybridization in two related homoploid species can mix the genotypes which have the potential for good environmental adaptation conditions or rapid growth condition. Since hybridization technique has been used in other animals to produce more rapidly growing individuals, it may be useful in commercial fish culture. The nutritional composition and rapid growth rate of P. major, A. schlegelii and hybrid F1 had been researched. However, gene expressions of these fish are less well studied. de novo assembly RNA-Seq is a better approach to understanding transcriptomes of animals and can offer much data with better coverage and sufficient sequence depth for transcriptomes. Results: In order to facilitate molecular research in parents and hybrids F1, we characterized the whole body transcriptome for identifcation of transcripts involved in growth, metabolism and immune since several attributes were coming from different samples (Acanthopagrus schlegelii, Pagrus major and hybrid F1 Acanthopagrus schlegelii ♂× Pagrus major ♀). We analyzed the transcriptome of As, Pm and hybrid F1 AP using Illumina high throughput sequencing platform. Our results suggested that physiological index of organism development we observed is consistent to the gene express in transcriptome. We have also compared the expression levels of transcripts in parents and hybrids F1. The results showed that AP had a quickly growth and strong resistant than parents Pm and As. Conclusion: This is the first research on transcriptome of As, Pm and hybrid F1 at one month age. And it will provide an important basic molecular data for studying molecular mechanisms involved in different sample.

scholarly journals Bioinformatic Analysis of Gene Variants from Gastroschisis Recurrence Identifies Multiple Novel Pathogenetic Pathways: Implication for the Closure of the Ventral Body Wall

2019 ◽  
Vol 20 (9) ◽  
pp. 2295 ◽  
Author(s):  
Víctor M. Salinas-Torres ◽  
Hugo L. Gallardo-Blanco ◽  
Rafael A. Salinas-Torres ◽  
Ricardo M. Cerda-Flores ◽  
José J. Lugo-Trampe ◽  
...  
Keyword(s):  
Biological Networks ◽  
Body Wall ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Developmental Process ◽  
Interaction Analysis ◽  
Regulation Of Gene Expression ◽  
Bioinformatic Analysis ◽  
Recessive Model ◽  
Functional Enrichment

We investigated whether likely pathogenic variants co-segregating with gastroschisis through a family-based approach using bioinformatic analyses were implicated in body wall closure. Gene Ontology (GO)/Panther functional enrichment and protein-protein interaction analysis by String identified several biological networks of highly connected genes in UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT1A10, AOX1, NOTCH1, HIST1H2BB, RPS3, THBS1, ADCY9, and FGFR4. SVS–PhoRank identified a dominant model in OR10G4 (also as heterozygous de novo), ITIH3, PLEKHG4B, SLC9A3, ITGA2, AOX1, and ALPP, including a recessive model in UGT1A7, UGT1A6, PER2, PTPRD, and UGT1A3. A heterozygous compound model was observed in CDYL, KDM5A, RASGRP1, MYBPC2, PDE4DIP, F5, OBSCN, and UGT1A. These genes were implicated in pathogenetic pathways involving the following GO related categories: xenobiotic, regulation of metabolic process, regulation of cell adhesion, regulation of gene expression, inflammatory response, regulation of vascular development, keratinization, left-right symmetry, epigenetic, ubiquitination, and regulation of protein synthesis. Multiple background modifiers interacting with disease-relevant pathways may regulate gastroschisis susceptibility. Based in our findings and considering the plausibility of the biological pattern of mechanisms and gene network modeling, we suggest that the gastroschisis developmental process may be the consequence of several well-orchestrated biological and molecular mechanisms which could be interacting with gastroschisis predispositions within the first ten weeks of development.

scholarly journals Genome sequencing of Aspergillus glaucus ‘CCHA’ provides insights into salt-stress adaptation

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8609
Author(s):  
Wenmin Qiu ◽  
Jingen Li ◽  
Yi Wei ◽  
Feiyu Fan ◽  
Jing Jiang ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Redox State ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
De Novo ◽  
Natural Environments ◽  
Isolation And Identification ◽  
Microbial Genomes ◽  
Aspergillus Glaucus ◽  
Survey Analyses

Aspergillus, as a genus of filamentous fungi, has members that display a variety of different behavioural strategies, which are affected by various environmental factors. The decoded genomic sequences of many species vary greatly in their evolutionary similarities, encouraging studies on the functions and evolution of the Aspergillus genome in complex natural environments. Here, we present the 26 Mb de novo assembled high-quality reference genome of Aspergillus glaucus ‘China Changchun halophilic Aspergillus’ (CCHA), which was isolated from the surface of plants growing near a salt mine in Jilin, China, based on data from whole-genome shotgun sequencing using Illumina Solexa technology. The sequence, coupled with data from comprehensive transcriptomic survey analyses, indicated that the redox state and transmembrane transport might be critical molecular mechanisms for the adaptation of A. glaucus ‘CCHA’ to the high-salt environment of the saltern. The isolation of salt tolerance-related genes, such as CCHA-2114, and their overexpression in Escherichia coli demonstrated that A. glucus ‘CCHA’ is an excellent organism for the isolation and identification of salt tolerant-related genes. These data expand our understanding of the evolution and functions of fungal and microbial genomes, and offer multiple target genes for crop salt-tolerance improvement through genetic engineering.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

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