scholarly journals Transcriptomic responses to drought stress in Polygonatum kingianum tuber

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Huali Qian ◽  
Zhe Xu ◽  
Kun Cong ◽  
Xinyan Zhu ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Expression Profiles ◽  
Lignin Biosynthesis ◽  
Carotenoid Biosynthesis ◽  
Flavonoid Biosynthesis ◽  
Differentially Expressed ◽  
Severe Drought ◽  
Galactose Metabolism ◽  
Phenylpropanoid Biosynthesis ◽  
Transcriptome Resource

Abstract Background Polygonatum kingianum Coll. et Hemsl. is an important plant in Traditional Chinese Medicine. The extracts from its tubers are rich in polysaccharides and other metabolites such as saponins. It is a well-known concept that growing medicinal plants in semi-arid (or drought stress) increases their natural compounds concentrations. This study was conducted to explore the morpho-physiological responses of P. kingianum plants and transcriptomic signatures of P. kingianum tubers exposed to mild, moderate, and severe drought and rewatering. Results The stress effects on the morpho-physiological parameters were dependent on the intensity of the drought stress. The leaf area, relative water content, chlorophyll content, and shoot fresh weight decreased whereas electrolyte leakage increased with increase in drought stress intensity. A total of 53,081 unigenes were obtained; 59% of which were annotated. We observed that 1352 and 350 core genes were differentially expressed in drought and rewatering, respectively. Drought stress driven differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, starch and sucrose metabolism, and stilbenoid diarylheptanoid and gingerol biosynthesis, and carotenoid biosynthesis pathways. Pathways such as plant-pathogen interaction and galactose metabolism were differentially regulated between severe drought and rewatering. Drought reduced the expression of lignin, gingerol, and flavonoid biosynthesis related genes and rewatering recovered the tubers from stress by increasing the expression of the genes. Increased expression of carotenoid biosynthesis pathway related genes under drought suggested their important role in stress endurance. An increase in starch and sucrose biosynthesis was evident from transcriptomic changes under drought stress. Rewatering recovered the drought affected tubers as evident from the contrasting expression profiles of genes related to these pathways. P. kingianum tuber experiences an increased biosynthesis of sucrose, starch, and carotenoid under drought stress. Drought decreases the flavonoids, phenylpropanoids, gingerol, and lignin biosynthesis. These changes can be reversed by rewatering the P. kingianum plants. Conclusions These results provide a transcriptome resource for P. kingianum and expands the knowledge on the effect of drought and rewatering on important pathways. This study also provides a large number of candidate genes that could be manipulated for drought stress tolerance and managing the polysaccharide and secondary metabolites’ contents in P. kingianum.

scholarly journals Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.)

2020 ◽  
Vol 21 (22) ◽  
pp. 8520
Author(s):  
Ling Qin ◽  
Erying Chen ◽  
Feifei Li ◽  
Xiao Yu ◽  
Zhenyu Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Drought Stress ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Foxtail Millet ◽  
Gene Expression Profiles ◽  
Sugar Metabolism ◽  
Setaria Italica ◽  
Phenylpropanoid Biosynthesis

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop because of its health benefits and adaptation to drought stress; however, reports of transcriptomic analysis of genes responding to re-watering after drought stress in foxtail millet are rare. The present study evaluated physiological parameters, such as proline content, p5cs enzyme activity, anti-oxidation enzyme activities, and investigated gene expression patterns using RNA sequencing of the drought-tolerant foxtail millet variety (Jigu 16) treated with drought stress and rehydration. The results indicated that drought stress-responsive genes were related to many multiple metabolic processes, such as photosynthesis, signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, and osmotic adjustment. Furthermore, the Δ1-pyrroline-5-carboxylate synthetase genes, SiP5CS1 and SiP5CS2, were remarkably upregulated in foxtail millet under drought stress conditions. Foxtail millet can also recover well on rehydration after drought stress through gene regulation. Our data demonstrate that recovery on rehydration primarily involves proline metabolism, sugar metabolism, hormone signal transduction, water transport, and detoxification, plus reversal of the expression direction of most drought-responsive genes. Our results provided a detailed description of the comparative transcriptome response of foxtail millet variety Jigu 16 under drought and rehydration environments. Furthermore, we identify SiP5CS2 as an important gene likely involved in the drought tolerance of foxtail millet.

scholarly journals Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 30
Author(s):  
Yaodong Zhao ◽  
Wenjing Ma ◽  
Xiaohong Wei ◽  
Yu Long ◽  
Ying Zhao ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Drought Stress ◽  
Medicago Sativa ◽  
High Throughput ◽  
Drought Resistance ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Medicago Sativa L

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

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 Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress inBrassica rapaL. (Inbred Line “Chiifu”)

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Soon-Wook Kwon ◽  
Mijeong Kim ◽  
Hijin Kim ◽  
Joohyun Lee
Keyword(s):  
Drought Stress ◽  
Inbred Line ◽  
Stress Responses ◽  
Target Genes ◽  
Antioxidant Activities ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Family Protein

Through a comparative shotgun quantitative proteomics analysis inBrassica rapa(inbred line Chiifu), total of 3,009 nonredundant proteins were identified with a false discovery rate of 0.01 in 3-week-old plants subjected to dehydration treatment for 0, 24, and 48 h, plants subjected to drought stress. Ribulose-bisphosphate carboxylases, chlorophyll a/b-binding protein, and light harvesting complex in photosystem II were highly abundant proteins in the leaves and accounted for 9%, 2%, and 4%, respectively, of the total identified proteins. Comparative analysis of the treatments enabled detection of 440 differentially expressed proteins during dehydration. The results of clustering analysis, gene ontology (GO) enrichment analysis, and analysis of composite expression profiles of functional categories for the differentially expressed proteins indicated that drought stress reduced the levels of proteins associated with photosynthesis and increased the levels of proteins involved in catabolic processes and stress responses. We observed enhanced expression of many proteins involved in osmotic stress responses and proteins with antioxidant activities. Based on previously reported molecular functions, we propose that the following five differentially expressed proteins could provide target genes for engineering drought resistance in plants: annexin, phospholipase D delta, sDNA-binding transcriptional regulator, auxin-responsive GH3 family protein, and TRAF-like family protein.

scholarly journals Identification of Genes/Proteins Related to Submergence Tolerance by Transcriptome and Proteome Analyses in Soybean

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yanhui Lin ◽  
Wei Li ◽  
Yanwei Zhang ◽  
Changjian Xia ◽  
Yun Liu ◽  
...  
Keyword(s):  
Lignin Biosynthesis ◽  
Differentially Expressed ◽  
Resistant Variety ◽  
Yield Reduction ◽  
Submergence Tolerance ◽  
Anaerobic Conditions ◽  
Kegg Pathways ◽  
Production Practice ◽  
Submergence Stress ◽  
Phenylpropanoid Biosynthesis

Abstract Flooding can lead to yield reduction of soybean. Therefore, identification of flooding tolerance genes has great significance in production practice. In this study, Qihuang 34, a highly-resistant variety to flooding stress, was selected for submergence treatments. Transcriptome and proteome analyses were conducted, by which twenty-two up-regulated differentially expressed genes (DEGs)/differentially expressed proteins (DEPs) associated with five KEGG pathways were isolated. The number of the DEGs/DEPs enriched in glycolysis/gluconeogenesis was the highest. Four of these genes were confirmed by RT-qPCR, suggesting that glycolysis/gluconeogenesis may be activated to generate energy for plant survival under anaerobic conditions. Thirty-eight down-regulated DEGs/DEPs associated with six KEGG pathways were identified under submergence stress. Eight DEGs/DEPs enriched in phenylpropanoid biosynthesis were assigned to peroxidase, which catalyzes the conversion of coumaryl alcohol to hydroxy-phenyl lignin in the final step of lignin biosynthesis. Three of these genes were confirmed by RT-qPCR. The decreased expression of these genes led to the inhibition of lignin biosynthesis, which may be the cause of plant softening under submergence stress for a long period of time. This study revealed a number of up-/down-regulated pathways and the corresponding DEGs/DEPs, by which, a better understanding of the mechanisms of submergence tolerance in soybean may be achieved.

scholarly journals Comparative RNA-Sequence Transcriptome Analysis of Phenolic Acid Metabolism in Salvia miltiorrhiza, a Traditional Chinese Medicine Model Plant

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Zhenqiao Song ◽  
Linlin Guo ◽  
Tian Liu ◽  
Caicai Lin ◽  
Jianhua Wang ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Phenolic Acid ◽  
Expression Profiles ◽  
Salvia Miltiorrhiza ◽  
Lignin Biosynthesis ◽  
Biosynthesis Pathway ◽  
Acid Biosynthesis ◽  
The Core ◽  
Phenylpropanoid Biosynthesis

Salvia miltiorrhiza Bunge is an important traditional Chinese medicine (TCM). In this study, two S. miltiorrhiza genotypes (BH18 and ZH23) with different phenolic acid concentrations were used for de novo RNA sequencing (RNA-seq). A total of 170,787 transcripts and 56,216 unigenes were obtained. There were 670 differentially expressed genes (DEGs) identified between BH18 and ZH23, 250 of which were upregulated in ZH23, with genes involved in the phenylpropanoid biosynthesis pathway being the most upregulated genes. Nine genes involved in the lignin biosynthesis pathway were upregulated in BH18 and thus result in higher lignin content in BH18. However, expression profiles of most genes involved in the core common upstream phenylpropanoid biosynthesis pathway were higher in ZH23 than that in BH18. These results indicated that genes involved in the core common upstream phenylpropanoid biosynthesis pathway might play an important role in downstream secondary metabolism and demonstrated that lignin biosynthesis was a putative partially competing pathway with phenolic acid biosynthesis. The results of this study expanded our understanding of the regulation of phenolic acid biosynthesis in S. miltiorrhiza.

scholarly journals Drought-induced ABA, H2O2 and JA positively regulate CmCAD genes and lignin synthesis in melon stems

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Wei Liu ◽  
Yun Jiang ◽  
Yazhong Jin ◽  
Chenghui Wang ◽  
Juan Yang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Expression Profiles ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Signal Molecules ◽  
Lignin Synthesis ◽  
Enzyme Functions ◽  
Stress Promoter ◽  
Important Enzyme

Abstract Background Cinnamyl alcohol dehydrogenase (CAD) is an important enzyme functions at the last step in lignin monomer synthesis pathway. Our previous work found that drought induced the expressions of CmCAD genes and promoted lignin biosynthesis in melon stems. Results Here we studied the effects of abscisic acid (ABA), hydrogen peroxide (H2O2) and jasmonic acid (JA) to CmCADs under drought stress. Results discovered that drought-induced ABA, H2O2 and MeJA were prevented efficiently from increasing in melon stems pretreated with fluridone (Flu, ABA inhibitor), imidazole (Imi, H2O2 scavenger) and ibuprofen (Ibu, JA inhibitor). ABA and H2O2 are involved in the positive regulations to CmCAD1, 2, 3, and 5, and JA is involved in the positive regulations to CmCAD2, 3, and 5. According to the expression profiles of lignin biosynthesis genes, ABA, H2O2 and MeJA all showed positive regulations to CmPAL2-like, CmPOD1-like, CmPOD2-like and CmLAC4-like. In addition, positive regulations were also observed with ABA to CmPAL1-like, CmC4H and CmCOMT, with H2O2 to CmPAL1-like, CmC4H, CmCCR and CmLAC17-like, and with JA to CmCCR, CmCOMT, CmLAC11-like and CmLAC17-like. As expected, the signal molecules positively regulated CAD activity and lignin biosynthesis under drought stress. Promoter::GUS assays not only further confirmed the regulations of the signal molecules to CmCAD1~3, but also revealed the important role of CmCAD3 in lignin synthesis due to the strongest staining of CmCAD3 promoter::GUS. Conclusions CmCADs but CmCAD4 are positively regulated by ABA, H2O2 and JA under drought stress and participate in lignin synthesis.

scholarly journals Combination of RNA-Seq transcriptomics and iTRAQ proteomics reveal the mechanism involved in fresh-cut yam yellowing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shuang Guo ◽  
Dan Wang ◽  
Yue Ma ◽  
Yan Zhang ◽  
Xiaoyan Zhao
Keyword(s):  
Tricarboxylic Acid Cycle ◽  
Carotenoid Biosynthesis ◽  
Differentially Expressed ◽  
Biosynthesis Pathway ◽  
Total Carotenoids ◽  
Phenylpropanoid Biosynthesis ◽  
Itraq Proteomics ◽  
Carotenoid Biosynthesis Pathway ◽  
Fresh Cut ◽  
Yellow Pigments

AbstractThe aim of this study was to examine the regulation of transcriptomics and proteomics related to the yellowing of fresh-cut yams after storage. The comparison of yellow fresh-cut yam (YFY) vs. white fresh-cut yam (control) revealed 6894 upregulated and 6800 downregulated differentially expressed genes along with 1277 upregulated and 677 downregulated differentially expressed proteins. The results showed that the total carotenoids, flavonoids, and bisdemethoxycurcumin in YFY were higher than in the control due to the significant up-regulation of critical genes in the carotenoid biosynthesis pathway, flavonoid biosynthesis pathway, and stilbenoid, diarylheptanoid, and gingerol biosynthesis pathway. In addition, the tricarboxylic acid cycle and phenylpropanoid biosynthesis were both enhanced in YFY compared to the control, providing energy and precursors for the formation of yellow pigments. The results suggest that the synthesis of yellow pigments is regulated by critical genes, which might explain the yellowing of fresh-cut yam after storage.

scholarly journals Transcriptomic Analysis for the Identification of Metabolic Pathway Genes Related to Toluene Response in Ardisia pusilla

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1011
Author(s):  
Junping Xu ◽  
Chang Ho Ahn ◽  
Ju Young Shin ◽  
Pil Man Park ◽  
Hye Ryun An ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Differentially Expressed Gene ◽  
Carotenoid Biosynthesis ◽  
Raw Material ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Quantitative Real Time Pcr ◽  
Phenylpropanoid Biosynthesis ◽  
Differential Gene

Toluene is an industrial raw material and solvent that can be found abundantly in our daily life products. The amount of toluene vapor is one of the most important measurements for evaluating air quality. The evaluation of toluene scavenging ability of different plants has been reported, but the mechanism of plant response to toluene is only partially understood. In this study, we performed RNA sequencing (RNA-seq) analysis to detect differential gene expression in toluene-treated and untreated leaves of Ardisiapusilla. A total of 88,444 unigenes were identified by RNA-seq analysis, of which 49,623 were successfully annotated and 4101 were differentially expressed. Gene ontology analysis revealed several subcategories of genes related to toluene response, including cell part, cellular process, organelle, and metabolic processes. We mapped the main metabolic pathways of genes related to toluene response and found that the differentially expressed genes were mainly involved in glycolysis/gluconeogenesis, starch and sucrose metabolism, glycerophospholipid metabolism, carotenoid biosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis. In addition, 53 transcription factors belonging to 13 transcription factor families were identified. We verified 10 differentially expressed genes related to metabolic pathways using quantitative real-time PCR and found that the results of RNA-seq were positively correlated with them, indicating that the transcriptome data were reliable. This study provides insights into the metabolic pathways involved in toluene response in plants.

scholarly journals Analysis of differentially expressed genes induced by drought stress in tef (Eragrostistef) root

2020 ◽  
Vol 36 (2) ◽  
pp. 167-187
Author(s):  
Hewan Demissie Degu
Keyword(s):  
Drought Stress ◽  
Root Growth ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Eragrostis Tef ◽  
Direct Role ◽  
Functional Roles ◽  
Related Transcription Factor

Drought stress is one of the major abiotic stresses which induces root growth in tef. Molecular mechanisms underlying the elongation of roots under drought stress are not known. Therefore, we aimed to study the tef root system to uncover the expression profiles for drought stress using Agilent gene chip of rice. One hundred seventy-five expressed genes were found to be differentially expressed after eight days of drought stress with Eragrostis tef- resistant genotype, Kaye Murri. The drought-responsive genes were isolated and classified into nine categories according to the functional roles in plant metabolic pathways, such as defense, signal transduction, cell wall fortification, oxidative stress, photosynthesis,  development, cell maintenance, RNA binding, and unknown functions. The profiles of tef root genes, responsive to drought stress shared common identities with other expression profiles known to be elicited by diverse stresses, including pathogenesis, abiotic stress, and wounding. Well-known drought-related transcription factor-like, WRKY and bHLH were up-regulated. Cell transport-related regulators such as potassium transporter 22-like, auxin transporter-like protein 1, and wall-associated receptor kinase were also involved in the expression profile of tef root under drought stress. Their expression had enhanced the drought-responsive genes, which, have a direct role to maintain root growth under drought stress. Key words: Drought, Genome, Microarray, Root, Tef

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