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Full-length transcriptome of Glycyrrhiza uralensis Fisch. in under eight treatment

ABSTRACT: Purpose: The goal of this study are to reveal the internal mechanism of silicon increased Glycyrrhiza uralensis Fisch. seedlings drought-tolerance,salt-tolerance and salt-drought tolerance by RNA-Seq. Methods: mRNA profiles of Glycyrrhiza uralensis Fisch. Seedling in eight treatment: control treatment with or without silicon,salt treatment with or without silicon,drought treatment with or without silicon,salt-drought treatment with or without silicon. Each treatment group sequenced the aerial (stems, leaves, buds and all the above ground parts) and underground parts (roots and all the underground parts) respectively Results:A total of 48 samples were sequenced and 372.37GB of clean data was acquired. The clean data of every sample reached 5.96GB, and the percentage of Q30 base was 94.63% or above. Clean reads of each sample were sequentially aligned with the specified reference genome, and alignment efficiency ranged from 85.27% to 92.66%. Therefore, the transcriptome data of samples were obtained with a high correct rate and good genomic coverage.Results of sequencing analysis showed that compared with CK group, there were 1426 DEGs (771 up-regulated and 655 down-regulated), 1386 DEGs (571 up-regulated and 815 down-regulated) and 4192 DEGs (1668 up-regulated and 2524 down-regulated) in aerial part, and 1462 DEGs (730 up-regulated and 732 down-regulated), 2212 DEGs (939 up-regulated and 1273 down-regulated) and 3735 DEGs (1768 up-regulated and 1986 down-regulated) in underground part of D, S and SD group respectively. Conclusions: Our study help to better understand the underlying molecular mechanisms of silicon improve the drought-tolerance,salt-tolerance and salt-drought tolerance of G. uralensis.

ORGANISM(S): Glycyrrhiza uralensis

PROVIDER: GSE197004 | GEO | 2022/02/21

REPOSITORIES: GEO

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Full-length transcriptome of Glycyrrhiza uralensis Fisch. in under five treatment

Project description:Purpose: The goal of this study are to reveal the internal mechanism of Bacillus pumilus G5 and silicon increased Glycyrrhiza uralensis Fisch. seedlings drought-tolerance by RNA-Seq. Methods: mRNA profiles of Glycyrrhiza uralensis Fisch. Seedling in five treatment: control treatment, drought stress treatment, drought stress with G5 treatment, drought stress with Si treatment and drought stress with G5 combined Si treatment. Results: The full-length transcriptome sequencing of 15 samples was completed, and the clean data of each sample was 6.28GB. All the consistent transcript sequences were aligned to the reference genome by minimap2 software and then de-redundant analysis was performed. Finally, 37267 genes were obtained. A total of 6934 DEGs were identified in four comparisons (D vs CK, DB vs D, DSi vs D, and DBSi vs D), among which are 967, 1559, 1278 and 3130 DEGs in four comparisons, respectively. Conclusions: Our study help to better understand the underlying molecular mechanisms of Bacillus pumilus G5 and silicon improve the drought-tolerance of G. uralensis.

2022-09-30 | GSE214347 | GEO

Analysis of whole transcriptome RNA-seq data reveals the involvement of alternative splicing in the drought response of Glycyrrhiza uralensis

Project description:we performed a genome-wide analysis of AS events in G. uralensis at different time points under drought stress using a high-throughput RNA sequencing approach. We detected 2479 and 2764 AS events in the aerial part (AP) and underground part (UP), respectively, of drought-stressed G. uralensis. Of these, last exon variable shear and exon skipping were the main types of AS. Overall, 2653 genes undergoing significant AS regulation were identified from the AP and UP of G. uralensis exposed to drought for 2, 6, 12, and 24 h. Gene Ontology analyses indicated that AS plays an important role in the regulation of nitrogen and protein metabolism in the drought response of G. uralensis. Notably, the spliceosomal pathway and basal transcription factor pathway were significantly enriched with differentially spliced genes (DSGs) under drought stress. Genes related to splicing regulators in the AP and UP of G. uralensis responded to drought stress and themselves underwent AS under drought conditions. In summary, our data suggest that drought-responsive AS directly and indirectly regulates the drought response of G. uralensis. Further in-depth studies on the functions and mechanisms of AS during abiotic stresses will provide new strategies for improving plant stress resistance.

2022-04-20 | GSE197490 | GEO

Full-length transcriptome of Glycyrrhiza uralensis Fisch. in under four treatment

Project description:Purpose: The goal of this study are to reveal the internal mechanism of Bacillus cereus G2 increased Glycyrrhiza uralensis Fisch. seedlings salt-tolerance by RNA-Seq. Methods: mRNA profiles of Glycyrrhiza uralensis Fisch. Seedling in four treatment: control treatment, G2 treatment, salt treatment, salt and G2 treatment. Results: We mapped about 3 million sequence reads per sample to the G. uralensis transcriptome. A total of 35,831 genes in all samples of G. uralensis were identified and quantified by transcriptions, among which 3608 DEGs were identified. There are 1589, 623, 469 and 927 DEGs in S vs CK, CK+B vs CK, S+B vs S and S+B vs CK+B comparisons, respectively. Validation of expression levels for 12 randomly selected DEG candidates was carried out by quantitative real-time PCR (qRT-PCR). The results showed high congruence between RNA-Seq and qRT-PCR results (coefficient of determination R2 =0.9088) indicating the reliability of RNA-Seq quantification of gene expression. Conclusions: Our study help to better understand the underlying molecular mechanisms of G2 improve the salt tolerance of G. uralensis.

2021-12-30 | GSE187003 | GEO

Transcriptomic dynamics provides an insight into the mechanism for silicon-mediated alleviation of salt stress in cucumber plants

Project description:Salinity seriously reduces the yield and quality of crops. Silicon (Si) has been widely reported to have beneficial effects on plant growth and development under salt stress. However, the mechanism is still poorly understood. In an attempt to identify genes or gene networks that may be orchestrated to improve salt tolerance of cucumber plants, we profiled the RNA-seq transcriptomes of both control and salt-stressed cucumber leaves in the presence or absence of added Si. The comparative transcriptome analysis revealed that Si plays an important role in shaping the transcriptome of cucumber: the expression levels of >1,000 genes (differtially expressed genes, DEGs) were changed in response to Si treatment as compared with the control, and these genes were mainly involved in ion transport, hormone and signal transduction, biosynthesis and metabolic processes, stress and defense responses, and antioxidant activity. Under salt stress, many genes functionally associated with metabolic processes and responses to environmental stimuli were strongly up- or down-regulated in their expressions. Si treatment showed a tendency that induced the transcriptomic profile of salt-stressed cucumber back to that of the control with large majority of Na down-regulated DEGs and about half of Na up-regulated DEGs being adjusted back to CT levels. This study provides a novel insight into the mechanism for Si-mediated alleviation of salt stress in plants at the transcriptome level, and it suggests that Si may act as an elicitor to precondition cucumber plants and induce salt tolerance.

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2017-04-22 | E-GEOD-56964 | biostudies-arrayexpress

Microarray of young shoot of Populus trichocarpa under abiotic stresses

Project description:We identified 1251 and 1509 significantly up-regulated and down-regulated genes, respectively (FDR<0.05) by drought-treatment. In contrast, in response to salt stress, only 133 genes and 309 genes were significantly up- and down-regulated (FDR<0.05) respectively. Of these, 55% of the up-regulated and 75% of the down-regulated genes were also identified in the drought data set.

2018-12-30 | GSE124496 | GEO

Transcriptome analysis of salt stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.)

Project description:Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.

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Gene expression data of winter wheat root under drought stress for 7 days by two phosphorus treatments

Project description:A complex regulatory network is the mechanism of wheat roots responding to drought stress at low and adequate phosphorus levels. The transcription levels of genes encoding silicon transporters, phosphate transporters, sucrose synthesis, etc., are mostly up-regulated in Xindong20. The genes encoding the electron transport chain and the respiratory chain are mostly down-regulated in Xindong23. These results suggest that wheat roots should maintain the structural integrity of the cells and reduce the energy metabolism during the coupled stress of drought and low phosphorus, which will help to improve the drought tolerance of wheat. The objective of the present data was to increase the information about the effect of drought on the transcriptomes of wheat root cultured by two phosphorus levels.

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Whole genome-wide expression profiles of hemp (Cannabis sativa L.) in response to drought stress

2017-04-22 | GSE56964 | GEO

Response to drought and salt stress in leaves of poplar (Populus alba M-CM-^W P. glandulosa): Expression profiling by oligonucleotide microarray analysis

Project description:We performed that comprehensive identification of genes responsible for stress tolerance by analyzing the whole-genome expression profiles of poplar (Populus alba M-CM-^W P. glandulosa) leaves exposed to drought and salt stresses. Examination at the molecular level how this tree species responds to drought and salt stresses by regulating the expression of genes involved in signal transduction, transcriptional regulation, and stress responses. Genome-wide analysis was conducted in poplar leaves exposed to drought and salt stresses.The plants were acclimated in soil and grown for 6 weeks in controlled conditions in a growth room (16 h light; light intensity, 150 M-NM-<mol m-2sec-1; 24M-BM-0C). Plants with a height of about 15 cm were separately exposed to either drought or salt stress. Up- and down-regulated genes were identified, and their putative functions are discussed.

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