Transcriptomic study (RNAseq) of diurnal expression of Brachypodium distachyon ecotypes Bd21 and Bd21-3 under submergence stress
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ABSTRACT:
PROVIDER: PRJNA889013 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21853500.fastq.gz | Fastqsanger.gz | |||
| SRR21853501.fastq.gz | Fastqsanger.gz | |||
| SRR21853502.fastq.gz | Fastqsanger.gz | |||
| SRR21853503.fastq.gz | Fastqsanger.gz | |||
| SRR21853504.fastq.gz | Fastqsanger.gz |
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Project description:To study the diurnal transcriptome (RNA-seq) expressed by the monocot model plant B. distachyon under submergence stress, we analyzed two different ecotypes (Bd21, submergence sensitive; Bd21-3, submergence tolerant) at 5 different time points (dawn, ZT0; midday, ZT8; dusk, ZT16; middnight ZT20, end of night, ZT24).
2022-10-15 | GSE215159 | GEO
Project description:Purpose: The goal of this study is to compare the transcriptomes expressed during submergence stress of two Brachypodium distachyon ecotypes with contrasting survival under this stress. Bd21 is a submergence sensitive ecotype with EC50 of 2.5 days and Bd2-3 is a tolerant ecotype with EC50 of 4 days. Methods (Stress): Brachypodium Bd21 and Bd2-3 plants (14-day-old, 6 leaves stage) were submerged in a water column of 30 cm inside opaque-wall plastic tanks. Light still reached the plants at 40 μE m−2 s−1. Ecotypes were submerged side-by-side in a randomized manner; only plants submerged in the same tank were compared. Controls were grown in plastic tanks without a water column. Submergence stress started at ZT14 (2h before night, long-day regime 16h light, 8h dark). Above ground tissue was collected after 48 h submergence stress in liquid nitrogen and stored at -80ºC in an ultra freezer until further processing. Tissue was ground to powder with mortar, pestle and liquid nitrogen avoiding thawing. Control and submerged total RNA was extracted with TRIzol reagent (Invitrogen, 15596018), purified with Direct-zol RNA mini prep columns (Zymo Research, R2050) and digested in-column with DNAse I (ThermoScientific, #EN0521). RNA integrity and concentration was verified in denaturing 1.0% agarose gels, Nanodrop 2000 (ThermoScientific) and in a Bioanalyzer 2100 (Agilent) with the integrated software 2100 Expert, samples had a RNA Integrity Number (RIN) between 6.4-7.2 characteristic of aerial plant tissue (Babu and Gassman, 2011). Total RNA extracted from control and submerged tissue from three independent experiments consisting each of four individuals were used to construct cDNA indexed libraries and sequenced in a HiSeq2500 (Illumina) at 1x50 format, making a total of 12 sequenced libraries (tolerant and intolerant ecotype, control and submerged, all experimental triplicates) in a 2-lane format. RNA integrity, library construction and sequencing was performed as a service at the Unidad Universitaria de Secuenciación Masiva, Instituto de Biotecnología, Universidad Nacional Autónoma de México (IBT-UNAM).Differential Gene Expression (DGE) analysis was performed with edgeR using a generalized linear model and false discovery rate <0.05 (FDR). To group differentially expressed transcripts a logFC value of 1.5 (up-regulated) or -1.5 (down-regulated) and a FDR <0.05x10-5 were selected. GO analysis of differential transcripts was performed at phytozome.org Results: We identified commonly up-regulated genes (317) and exclusively up-regulated in Bd2-3 (466) or Bd21 (706). Regarding down-regulation, 330 transcripts were common, an exclusively 851 and 1026 for Bd2-3 and Bd21, respectively. GO analysis indicated that oxidative stress, pathogen responses and nitric oxide homeostasis were the most differential characteristics of tolerant ecotype Bd2-3. Conclusions: The use of triplicate RNAseq data of transcriptomes expressed in ecotypes with contrasting tolerance to submergence under long-day light regime, allowed us to identify common responsive routes such as SUSY, glycolysis, anaerobic routes (alanine, ethanol, lactate, GABA) and glyoxylate cycle. It also enabled us to discover integrated oxidative stress and NO homeostasis pathways that are differentially expressed in the tolerant ecotype. We expect that this information can be translated to agricultural relevant plants to increase our knowledge and biotechnological possibilities on plant submergence stress.
2016-01-04 | GSE74222 | GEO
Project description:Purpose: The goal of this study is to compare the transcriptomes expressed during submergence stress of two Brachypodium distachyon ecotypes with contrasting survival under this stress. Bd21 is a submergence sensitive ecotype with EC50 of 2.5 days and Bd2-3 is a tolerant ecotype with EC50 of 4 days. Methods (Stress): Brachypodium Bd21 and Bd2-3 plants (14-day-old, 6 leaves stage) were submerged in a water column of 30 cm inside opaque-wall plastic tanks. Light still reached the plants at 40 uE m-2 s-??1. Ecotypes were submerged side-by-side in a randomized manner; only plants submerged in the same tank were compared. Controls were grown in plastic tanks without a water column. Submergence stress started at ZT14 (2h before night, long-day regime 16h light, 8h dark). Above ground tissue was collected after 48 h submergence stress in liquid nitrogen and stored at -80C in an ultra freezer until further processing. Tissue was ground to powder with mortar, pestle and liquid nitrogen avoiding thawing. Control and submerged total RNA was extracted with TRIzol reagent (Invitrogen, 15596018), purified with Direct-zol RNA mini prep columns (Zymo Research, R2050) and digested in-column with DNAse I (ThermoScientific, EN0521). RNA integrity and concentration was verified in denaturing 1.0% agarose gels, Nanodrop 2000 (ThermoScientific) and in a Bioanalyzer 2100 (Agilent) with the integrated software 2100 Expert, samples had a RNA Integrity Number (RIN) between 6.4-7.2 characteristic of aerial plant tissue (Babu and Gassman, 2011). Total RNA extracted from control and submerged tissue from three independent experiments consisting each of four individuals were used to construct cDNA indexed libraries and sequenced in a HiSeq2500 (Illumina) at 1x50 format, making a total of 12 sequenced libraries (tolerant and intolerant ecotype, control and submerged, all experimental triplicates) in a 2-lane format. RNA integrity, library construction and sequencing was performed as a service at the Unidad Universitaria de Secuenciacion Masiva, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico (IBT-UNAM). Differential Gene Expression (DGE) analysis was performed with edgeR using a generalized linear model and false discovery rate <0.05 (FDR). To group differentially expressed transcripts a logFC value of 1.5 (up-regulated) or -1.5 (down-regulated) and a FDR <0.05x10-5 were selected. GO analysis of differential transcripts was performed at phytozome.org Results: We identified commonly up-regulated genes (317) and exclusively up-regulated in Bd2-3 (466) or Bd21 (706). Regarding down-regulation, 330 transcripts were common, an exclusively 851 and 1026 for Bd2-3 and Bd21, respectively. GO analysis indicated that oxidative stress, pathogen responses and nitric oxide homeostasis were the most differential characteristics of tolerant ecotype Bd2-3. Conclusions: The use of triplicate RNAseq data of transcriptomes expressed in ecotypes with contrasting tolerance to submergence under long-day light regime, allowed us to identify common responsive routes such as SUSY, glycolysis, anaerobic routes (alanine, ethanol, lactate, GABA) and glyoxylate cycle. It also enabled us to discover integrated oxidative stress and NO homeostasis pathways that are differentially expressed in the tolerant ecotype. We expect that this information can be translated to agricultural relevant plants to increase our knowledge and biotechnological possibilities on plant submergence stress. Sequenced libraries (triplicates, HiSeq2500 Illumina, 1x50 format) of aerial tissue (control and 48h submergence stress) of Brachypodium distachyon Bd21 (sensitive) and Bd2-3 (tolerant).
2016-01-04 | E-GEOD-74222 | biostudies-arrayexpress
Project description:SNF1 RELATED PROTEIN KINASE 1 (SnRK1) is proposed as a central integrator of regulatory pathways in plant stress and energy starvation signaling. We observed in this study that the Arabidopsis SnRK1.1 dominant negative mutant (SnRK1.1K48M) had lower tolerance to submergence than the wild-type, suggesting that SnRK1.1-dependent phosphorylation of target proteins is important in energy starvation signaling triggered by submergence. To gain further insight into submergence signaling mechanisms, we determined the temporal response to energy starvation through AMP/ATP quantification and used quantitative phosphoproteomics to compare the global changes in phosphopeptides in Col-0 and SnRK1.1K48M. We found that the phosphorylation levels of 59 peptides increased and the levels of 96 peptides decreased in Col-0 within 0.5�� h of submergence. Among the 59 peptides with increased phosphorylation in Col-0, 49 did not show increased phosphorylation levels in SnRK1.1K48M under submergence. These proteins are involved in sugar synthesis, glycolysis, osmotic regulation, ABA signaling, protein synthesis and ROS signaling. In particular, the phosphorylation of MAPK6, which is involved in regulating ROS responses under different abiotic stresses, was disrupted in the SnRK1.1K48M mutant. In addition, PTP1, a negative regulator of MAPK6 activity that directly dephosphorylates MAPK6, was also regulated by SnRK1.1. These results reveal insights into the function of SnRK1 and the downstream signaling factors of submergence.
2016-04-07 | PXD002353 | Pride
Project description:SNF1 RELATED PROTEIN KINASE 1 (SnRK1) is proposed as a central integrator of regulatory pathways in plant stress and energy starvation signaling. We observed in this study that the Arabidopsis SnRK1.1 dominant negative mutant (SnRK1.1K48M) had lower tolerance to submergence than the wild-type, suggesting that SnRK1.1-dependent phosphorylation of target proteins is important in energy starvation signaling triggered by submergence. To gain further insight into submergence signaling mechanisms, we determined the temporal response to energy starvation through AMP/ATP quantification and used quantitative phosphoproteomics to compare the global changes in phosphopeptides in Col-0 and SnRK1.1K48M. We found that the phosphorylation levels of 59 peptides increased and the levels of 96 peptides decreased in Col-0 within 0.5–3 h of submergence. Among the 59 peptides with increased phosphorylation in Col-0, 49 did not show increased phosphorylation levels in SnRK1.1K48M under submergence. These proteins are involved in sugar synthesis, glycolysis, osmotic regulation, ABA signaling, protein synthesis and ROS signaling. In particular, the phosphorylation of MAPK6, which is involved in regulating ROS responses under different abiotic stresses, was disrupted in the SnRK1.1K48M mutant. In addition, PTP1, a negative regulator of MAPK6 activity that directly dephosphorylates MAPK6, was also regulated by SnRK1.1. These results reveal insights into the function of SnRK1 and the downstream signaling factors of submergence.
2016-04-07 | PXD001815 | Pride
Project description:An indica rice cultivar FR13A, is widely grown as submergence tolerant variety and can withstand submergence up to two weeks. The tolerance is governed by a major QTL on chromosome 9 and represented as sub1. Recently the gene for sub1 has been mapped and cloned. However, the trait is governed by several QTLs and not by a single gene. To understand the mechanism of submergence tolerance we selected, two indica rice genotypes namely, I) FR13A, a tolerant indica variety and ii) IR24, a susceptible genotype for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under constitutive and submerged conditions at seedling stage. Keywords: Mechanism of submergence tolerance
2007-11-24 | GSE6362 | GEO
Project description:Arabidopsis plants display superior tolerance to submergence at the juvenile stage. We characterized the transcriptomic response to submergence in juvenile and adult plants. In this dataset, we include expression data from 2-week and 3-week old plants under dark air and dark submergence conditions.
2021-09-09 | GSE137866 | GEO
Project description:Most rice (Oryza sativa L.) cultivars die within several days of complete submergence, but some indica cultivars, such as FR13A, can survive up to 2 weeks of complete submergence. In FR13A, a major quantitative trait locus (QTL), named Sub1, provides mature plants with submergence tolerance. However, the Sub1 locus can not confer flooding tolerance during germination to FR13A. Another indica cultivar, Goda Heenati, shows both tolerance to flooding during germination and submergence in mature plants. It was once reported that submergence tolerance in FR13A and Goda Heenati cultivars was controlled by their respective genetic locus. These evidences indicate that tolerance to submergence in these two cultivars may involve differential mechanisms. To gain insight into their putatively differential responses to submergence stress, the Agilent rice genome 4×44 K oligonucleotide microarray was used to explore the transcriptome of FR13A and Goda Heenati under control and submergence-stressed conditions. Two-way ANOVA analysis with Benjamini-Hochberg false discovery rate demonstrated that at an overall P＜0.01 level, 2810, 8207, and 4 probes were significantly regulated for genotype, treatment, and genotype×treatment interaction, respectively. To identify statistically significant differentially expressed genes, a combined criterion of 2-fold or more change and unpaired t-test P value < 0.01 was uesd for both FR13A and Goda Heenati. A total of 504 probes were up-regulated and 592 probes were down-regulated in FR13A under submergence stress. In Goda Heenati, 998 probes were induced and 1186 probes were suppressed by submergence treatment.
2010-12-01 | GSE23574 | GEO
Project description:Analysis of the impact of plant growth regulators on submergence tolerance of rice at gene expression level. The hypothesis tested in the present study was that the submergence-tolerance was improved by foliar application of paclobutrazol under sumergence stress conditions.
2017-10-12 | GSE104035 | GEO
Project description:General translational repression is predicted as a key process to reduce energy consumption under hypoxia. We have previously showed that mRNA loading onto polysome is reduced in Arabidopsis under submergence. Here, we showed that plant stress activated GCN2 (general control nonderepressible 2) can phosphorylate eIF2a (Eukaryotic Initiation Factor 2a) in Arabidopsis under submergence, and this process is reversible after desubmergence. Compared to the wild-type, the reduction in polysome loading during submergence was less severe in the gcn2 mutant. Transgenic lines overexpressing GCN2 had more ATP and conferred better tolerance under submergence, suggesting that GCN2 might modulate the dynamics of translation to adjust the energy homeostasis under hypoxia. Interestingly, GCN2-eIF2a signaling was activated by ethylene under submergence. However, GCN2 activity was not affected in ein2-5 and eil1ein3 under submergence, suggesting that GCN2 activity was regulated by noncanonical ethylene signaling. In addition, the polysome loading was retained in both ein2-5 and etr1-1 under submergence, implying that ethylene modulated the dynamic translation under submergence via EIN2 and GCN2. Notably, our NGS analysis also demonstrated that EIN2 and GCN2 regulated the translation of 23 core hypoxia genes as well as 53% translational repressed genes under submergence. On the other hand, EIN2 and GCN2 also affected the expression of genes involved in hypoxic response, ethylene response, biotic stress and negative regulation of cytokinin signaling. Taken together, these demonstrated that entrapped ethylene triggers GCN2 and EIN2 to ensure the translation of stress required proteins under submergence and also provide a step stone for future investigation how eukaryotic cells modulate the translation to response for the changeable environments.
2022-06-08 | GSE149414 | GEO