scholarly journals Transcriptome Analyses in Different Cucumber Cultivars Provide Novel Insights into Drought Stress Responses

2018 ◽  
Vol 19 (7) ◽  
pp. 2067 ◽  
Author(s):  
Min Wang ◽  
Biao Jiang ◽  
Qingwu Peng ◽  
Wenrui Liu ◽  
Xiaoming He ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Stress Responses ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Water Deficiency ◽  
Sequencing Data ◽  
Aba Signal Transduction ◽  
Drought Tolerant ◽  
Sucrose Biosynthesis

Drought stress is one of the most serious threats to cucumber quality and yield. To gain a good understanding of the molecular mechanism upon water deficiency, we compared and analyzed the RNA sequencing-based transcriptomic responses of two contrasting cucumber genotypes, L-9 (drought-tolerant) and A-16 (drought-sensitive). In our present study, combining the analysis of phenotype, twelve samples of cucumber were carried out a transcriptomic profile by RNA-Seq under normal and water-deficiency conditions, respectively. A total of 1008 transcripts were differentially expressed under normal conditions (466 up-regulated and 542 down-regulated) and 2265 transcripts under drought stress (979 up-regulated and 1286 down-regulated). The significant positive correlation between RNA sequencing data and a qRT-PCR analysis supported the results found. Differentially expressed genes (DEGs) involved in metabolic pathway and biosynthesis of secondary metabolism were significantly changed after drought stress. Several genes, which were related to sucrose biosynthesis (Csa3G784370 and Csa3G149890) and abscisic acid (ABA) signal transduction (Csa4M361820 and Csa6M382950), were specifically induced after 4 days of drought stress. DEGs between the two contrasting cultivars identified in our study provide a novel insight into isolating helpful candidate genes for drought tolerance in cucumber.

scholarly journals Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Liang ◽  
Kunhua Wei ◽  
Fan Wei ◽  
Shuangshuang Qin ◽  
Chuanhua Deng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Small Rna ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Severe Drought ◽  
A Genome ◽  
Sophora Tonkinensis

Abstract Background Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. Results To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. Conclusion This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.

scholarly journals Drought Stress-Mediated Transcriptome Profile Reveals NCED as a Key Player Modulating Drought Tolerance in Populus davidiana

2021 ◽  
Vol 12 ◽  
Author(s):  
Sang-Uk Lee ◽  
Bong-Gyu Mun ◽  
Eun-Kyung Bae ◽  
Jae-Young Kim ◽  
Hyun-Ho Kim ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Stress Responses ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Transcriptional Level ◽  
Rna Seq ◽  
Drought Tolerant ◽  
Populus Davidiana ◽  
Strict Regulation

Populus trichocarpa has been studied as a model poplar species through biomolecular approaches and was the first tree species to be genome sequenced. In this study, we employed a high throughput RNA-sequencing (RNA-seq) mediated leaf transcriptome analysis to investigate the response of four different Populus davidiana cultivars to drought stress. Following the RNA-seq, we compared the transcriptome profiles and identified two differentially expressed genes (DEGs) with contrasting expression patterns in the drought-sensitive and tolerant groups, i.e., upregulated in the drought-tolerant P. davidiana groups but downregulated in the sensitive group. Both these genes encode a 9-cis-epoxycarotenoid dioxygenase (NCED), a key enzyme required for abscisic acid (ABA) biosynthesis. The high-performance liquid chromatography (HPLC) measurements showed a significantly higher ABA accumulation in the cultivars of the drought-tolerant group following dehydration. The Arabidopsis nced3 loss-of-function mutants showed a significantly higher sensitivity to drought stress, ~90% of these plants died after 9 days of drought stress treatment. The real-time PCR analysis of several key genes indicated a strict regulation of drought stress at the transcriptional level in the P. davidiana drought-tolerant cultivars. The transgenic P. davidiana NCED3 overexpressing (OE) plants were significantly more tolerant to drought stress as compared with the NCED knock-down RNA interference (RNAi) lines. Further, the NCED OE plants accumulated a significantly higher quantity of ABA and exhibited strict regulation of drought stress at the transcriptional level. Furthermore, we identified several key differences in the amino acid sequence, predicted structure, and co-factor/ligand binding activity of NCED3 between drought-tolerant and susceptible P. davidiana cultivars. Here, we presented the first evidence of the significant role of NCED genes in regulating ABA-dependent drought stress responses in the forest tree P. davidiana and uncovered the molecular basis of NCED3 evolution associated with increased drought tolerance.

Identification of Ubiquitin Ligase From Grapevine Ring C3H2C3E3 and Characterization of Drought Resistance Function of VyRCHC114

2020 ◽  
Author(s):  
Yihe Yu ◽  
Shengdi Yang ◽  
Lu Bian ◽  
Keke Yu ◽  
Xiangxuan Meng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Ubiquitin Ligase ◽  
Stress Responses ◽  
Phylogenetic Trees ◽  
Expression Profiles ◽  
E3 Ubiquitin Ligase ◽  
Pcr Analysis ◽  
Biotic And Abiotic Stress ◽  
Element Analysis

Abstract Background: RING is one of the largest E3 ubiquitin ligase families and C3H2C3 type is the largest subfamily of RING, playing an important role in plants’ development and growth and their biotic and abiotic stress responses. Results: A total of 143 RING C3H2C3-type genes (RCHCs) were discovered from the grapevine genome and separated into groups (I-XI) according to their phylogenetic analysis, with these genes named according to their positions on chromosomes. Gene replication analysis showed that tandem duplications play a predominant role in the expansion of VyRCHCs family together. Structural analysis showed that most VyRCHCs(67.13%) had no more than 2 introns, while genes clustered together based on phylogenetic trees had similar motifs and evolutionarily conserved structures. Cis-acting element analysis showed the diversity of VyRCHCs regulation. The expression profiles of eight DEGs in RNA-Seq after drought stress were similar to those in qRT-PCR analysis. The in vitro ubiquitin experiment showed that VyRCHC114 had E3 ubiquitin ligase activity, overexpression of VyRCHC114 in Arabidopsis improved drought tolerance, moreover, the transgenic plant survival rate increased by 30%, accompanied by changing of electrolyte leakage, chlorophyll content and the activities of SOD, POD, APX and CAT were changed. AtCOR15a, AtRD29A, AtERD15 and AtP5CS1 were expressed quantitatively, the results showed that they participated in the drought stress response may be regulated by the expression of VyRCHC114.Conclusions: Valuable new information on the evolution of grapevine RCHCs and its relevance for studying the functional characteristics of grapevine VyRCHC114 genes under drought stress emerged from this research.

scholarly journals Comparative Proteomics and Physiological Analyses Reveal Important Maize Filling-Kernel Drought-Responsive Genes and Metabolic Pathways

2019 ◽  
Vol 20 (15) ◽  
pp. 3743 ◽  
Author(s):  
Xuan Wang ◽  
Tinashe Zenda ◽  
Songtao Liu ◽  
Guo Liu ◽  
Hongyu Jin ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Protein Interactions ◽  
Stress Responses ◽  
Metabolic Pathways ◽  
Storage Proteins ◽  
Seed Storage Proteins ◽  
Comparative Proteomics ◽  
Venn Diagram ◽  
Drought Tolerant

Despite recent scientific headway in deciphering maize (Zea mays L.) drought stress responses, the overall picture of key proteins and genes, pathways, and protein–protein interactions regulating maize filling-kernel drought tolerance is still fragmented. Yet, maize filling-kernel drought stress remains devastating and its study is critical for tolerance breeding. Here, through a comprehensive comparative proteomics analysis of filling-kernel proteomes of two contrasting (drought-tolerant YE8112 and drought-sensitive MO17) inbred lines, we report diverse but key molecular actors mediating drought tolerance in maize. Using isobaric tags for relative quantification approach, a total of 5175 differentially abundant proteins (DAPs) were identified from four experimental comparisons. By way of Venn diagram analysis, four critical sets of drought-responsive proteins were mined out and further analyzed by bioinformatics techniques. The YE8112-exclusive DAPs chiefly participated in pathways related to “protein processing in the endoplasmic reticulum” and “tryptophan metabolism”, whereas MO17-exclusive DAPs were involved in “starch and sucrose metabolism” and “oxidative phosphorylation” pathways. Most notably, we report that YE8112 kernels were comparatively drought tolerant to MO17 kernels attributable to their redox post translational modifications and epigenetic regulation mechanisms, elevated expression of heat shock proteins, enriched energy metabolism and secondary metabolites biosynthesis, and up-regulated expression of seed storage proteins. Further, comparative physiological analysis and quantitative real time polymerase chain reaction results substantiated the proteomics findings. Our study presents an elaborate understanding of drought-responsive proteins and metabolic pathways mediating maize filling-kernel drought tolerance, and provides important candidate genes for subsequent functional validation.

Identification of Differentially Expressed and Spliced Genes with RNA Sequencing Analysis of CLL Specimens

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4582-4582
Author(s):  
Wei Liao ◽  
Gwen Jordaan ◽  
Artur Jaroszewicz ◽  
Matteo Pellegrini ◽  
Sanjai Sharma
Keyword(s):  
B Cells ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Fold Change ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Core Set

Abstract Abstract 4582 High throughput sequencing of cellular mRNA provides a comprehensive analysis of the transcriptome. Besides identifying differentially expressed genes in different cell types, it also provides information of mRNA isoforms and splicing alterations. We have analyzed two CLL specimens and a normal peripheral blood B cells mRNA by this approach and performed data analysis to identify differentially expressed and spliced genes. The result showed CLLs specimens express approximately 40% more transcripts compared to normal B cells. The FPKM data (fragment per kilobase of exon per million) revealed a higher transcript expression on chromosome 12 in CLL#1 indicating the presence of trisomy 12, which was confirmed by fluorescent in-situ hybridization assay. With a two-fold change in FPKM as a cutoff and a p value cutoff of 0.05 as compared to the normal B cell control, 415 genes and 174 genes in CLL#1 and 676 and 235 genes in CLL#2 were up and downregulated or differentially expressed. In these two CLL specimens, 45% to 75% of differentially expressed genes are common to both the CLL specimens indicating that genetically disparate CLL specimens have a high percentage of a core set of genes that are potentially important for CLL biology. Selected differentially expressed genes with increased expression (selectin P ligand, SELPLG, and adhesion molecule interacts with CXADR antigen 1, AMICA) and decreased (Fos, Jun, CD69 and Rhob) expression based on the FPKM from RNA-sequencing data were also analyzed in additional CLL specimens by real time PCR analysis. The expression data from RNA-seq closely matches the fold-change in expression as measured by RT-PCR analysis and confirms the validity of the RNA-seq analysis. Interestingly, Fos was identified as one of the most downregulated gene in CLL. Using the Cufflinks and Cuffdiff software, the splicing patterns of genes in CLL specimens and normal B cells were analyzed. Approximately, 1100 to 1250 genes in the two CLL specimens were significantly differentially spliced as compared to normal B cells. In this analysis as well, there is a core set of 800 common genes which are differentially spliced in the two CLL specimens. The RNA-sequencing analysis accurately identifies differentially expressed novel genes and splicing variations that will help us understand the biology of CLL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Genes, pathways and networks responding to drought stress in oil palm roots

2020 ◽  
Author(s):  
Le Wang ◽  
May Lee ◽  
baoqing Ye ◽  
Gen Hua Yue
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Ion Transport ◽  
Palm Oil ◽  
Stress Responses ◽  
Oil Palm ◽  
Metabolic Process ◽  
Differentially Expressed ◽  
Hormone Regulation ◽  
Transcriptomic Responses

Abstract Background: Palm oil is an important feedstock for biofuel. Palm oil yield is seriously affected by drought stress. However, not much is known about the molecular responses of oil palm to drought stress.Results: We studied the root transcriptomic responses of oil palm seedlings under normal culture and 14-day drought stress using RNA-seq and bioinformatics analysis. We identified 1293 differentially expressed genes (DEGs), involved in several molecular processes, such as cell wall biogenesis and functions, phenylpropanoid biosynthesis and metabolisms, ion transport and homeostasis and cellular ketone metabolic process, as well as small molecule biosynthetic process. We observed that DEGs were significantly enriched into the two categories: hormone regulation and metabolism, as well as ABC transporters. In addition, we identified three protein-protein interaction networks involved in the response to drought stress, including ion transport, reactive nitrogen species metabolic process and nitrate assimilation. Finally, 96 differentially expressed transcription factors were detected to be associated with drought stress response, which were classified into 28 families.Conclusions : The transcriptomic responses of oil palm seedlings to drought stress were systematically analysed, revealing important genes, pathways, networks and transcription factors involved in drought stress responses. These results provide new insights into the mechanisms of drought stress responses in economic crops. The genes and pathways identified in this study provide valuable genomic resources to improve drought tolerance of oil palm by both genetic modification and selective breeding.

scholarly journals Comparative analysis of combined phosphorus and drought stress-responses in two winter wheat

2020 ◽  
Author(s):  
Xiangchi Zhang ◽  
Weidan Lu ◽  
Xiaoli Wang ◽  
Bin Ma ◽  
Kaiyong Fu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Winter Wheat ◽  
Differentially Expressed Genes ◽  
Stress Responses ◽  
Differentially Expressed ◽  
Phosphorus Level ◽  
Root Tips ◽  
Percentage Content ◽  
Low Phosphorus

Abstract Phosphorus stress and drought stress are common abiotic stresses. In this study, two winter wheat “Xindong20” and “Xindong23” were solution cultured and then treated with drought stress under conventional phosphorus level (CP: 1.0 mmol/L) and low phosphorus level (LP: 0.05 mmol /L), respectively. The results showed that with the increase of drought stress, the LP application was more conducive to the growth of root tips, length, forks, surfarea and root vitality of wheat. Under the LP treatment, the total phosphorus content of root at rewatered 3d was increased by 94.2% in Xindong20 wheat and decreased by 48.9% in Xindong23 wheat, compared with their respective samples at drought 0d. The LP treatment increased the percentage content of K and decreased the P and Ca percentage content. However, under CP treatment, the percentage content of Zn after rewatered 3 days were increased, compared with drought 7d. Based on the GeneChip analysis of root samples from drought 7d, the microarray results showed that 4577 and 202 differentially expressed genes were detected from Xindong20 and Xindong23, respectively. Among them, 89.9% of differentially expressed genes were involved in organelles and vesicles in Xindong20, and 69.8% were involved in genes encoding root anatomical structure, respiratory chain, electron transport chain, ion transport and enzyme activity in Xindong23. Therefore, the supply of low phosphorus has more effects on the drought tolerance of wheat, and the wheat with different drought tolerance has different regulatory genes. The higher drought-tolerant wheat has more genes up-regulation in response to drought stress.

scholarly journals Physiological and Proteomic Analysis Revealed the Response Mechanisms of two Different Grought-resistant Maize Varieties

2021 ◽  
Author(s):  
Hongjie Li ◽  
Mei Yang ◽  
Chengfeng Zhao ◽  
Yifan Wang ◽  
Renhe Zhang
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Stress Responses ◽  
Molecular Chaperones ◽  
Electron Flow ◽  
Photochemical Efficiency ◽  
Growth And Yield ◽  
Protective Mechanism ◽  
Drought Tolerant ◽  
Maize Varieties

Abstract Background: Drought stress seriously limits the seedling growth and yield of maize. Despite previous studies on drought resistance mechanisms by which maize cope with water deficient, the link between physiological and molecular variations are largely unknown. To reveal the complex regulatory mechanisms, comparative physiology and proteomic analyses were conducted to investigate the stress responses of two maize cultivars with contrasting tolerance to drought stress. Results: Physiological results showed that SD609 (drought-tolerant) maintains higher photochemical efficiency by enhancing CEF (cyclic electron flow) protective mechanism and antioxidative enzymes activities. Proteomics analysis revealed a total of 198 and 102 proteins were differentially expressed in SD609 and SD902, respectively. Further enrichment analysis indicated that drought-tolerant ‘SD609’ increased the expression of proteins related to photosynthesis, antioxidants/detoxifying enzymes, molecular chaperones and metabolic enzymes. The up-regulation proteins related to PSII repair and photoprotection mechanisms resulted in more efficient photochemical capacity in tolerant variety under moderate drought. However, the drought-sensitive ‘SD902’ only induced molecular chaperones and sucrose synthesis pathways, and failed to protect the impaired photosystem. Further analysis indicated that proteins related to the electron transport chain, redox homeostasis and heat shock proteins (HSPs) could be important in protecting plants from drought stress. Conclusions: Our experiments explored the mechanism of drought tolerance, and obtained detailed information about the interconnection of physiological research and protein research. In summary, our findings could provide new clues into further understanding of drought tolerance mechanisms in maize.

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