Ontology highlight
ABSTRACT:
PROVIDER: PRJNA970414 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24472668_1.fastq.gz | Fastqsanger.gz | |||
| SRR24472668_2.fastq.gz | Fastqsanger.gz | |||
| SRR24472669_1.fastq.gz | Fastqsanger.gz | |||
| SRR24472669_2.fastq.gz | Fastqsanger.gz | |||
| SRR24472670_1.fastq.gz | Fastqsanger.gz |
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Project description:Real-time quantitative PCR (RT–qPCR) is the favoured method for gene expression analysis in molecular biology due to its sensitivity, specificity, cost-effectiveness, and reproducibility. To obtain the accuracy and reliability of RT-qPCR, the use of reliable reference genes is inevitable. There were many reports about the physiological response of giant reed (Arundo donax L.) to abiotic stresses. However, there is little use in the validation of reference genes under different treatments. It still belongs to the blank that the research about selecting reference genes under salt and alkali. In this study, the expression stability of twenty-three candidate reference genes in leaves and roots were assessed under salt, drought, and alkali stresses using geNorm, NormFinder, BestKeeper, and Delta Ct algorithms. Our results showed that no one gene had an invariant expression under different conditions. For example, under drought stress, UPL3, UBC2, and APT1 were better reference genes in leaves, RPL5 and FPS2 were better in roots. Under alkali stress, GAPDH, APT1, and RPS5 were better reference genes in leaves; UPL3, ACT2, and SAMDC2 were better in roots. In addition, the expression of MSD1 was used to further confirm the validated reference genes under salt, drought, and alkali stresses. It was proved that the use of inappropriate reference genes in giant reed significantly altered the relative expression of target genes and even reversed the results. Consequently, our results provided guidelines for reference gene selection under salt, drought, and alkali stresses and a foundation for more accurate and widespread use of RT-qPCR in the giant reed.
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Project description:Salt stress, especially saline-alkali stress, has seriously negative effect on citrus production. Ziyang xiangcheng (Citrus junos Sieb.) (Cj) has been reported as a saline-alkali stress and iron deficiency tolerant citrus rootstock. However, the molecular mechanism of its saline-alkali stress tolerance is still not clear. Two citrus rootstocks and one navel orange scion, Cj, Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) (Pt) and ‘Lane Late’ navel orange (Citrus sinensis (L.) Osb.) (LL), were used in this study. The grafted materials Cj+LL and Pt+LL grown in calcareous soil were used to identify genes and pathways responsive to saline-alkali stress using RNA-seq. The seedlings of Cj and Pt grown in the solutions with different gradient pH value were used to perform a supplement experiment. Comprehensively analyzing the data of RNA-seq, physiology and biochemistry, agronomic traits and mineral elements of Cj+LL, Pt+LL, Cj and Pt, several candidate pathways and genes were identified to be highly regulated under saline-alkali stress. Here, we propose citrate is important for the tolerance to iron deficiency and the jasmonate (JA) biosynthesis and signal transduction pathway may play a crucial role in tolerance to saline-alkali stress in citrus by interacting with other plant hormones, calcium signaling, ROS scavenging system and lignin biosynthesis.
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Project description:We present here a transcriptome dataset of millet seedling leaves based on RNA-seq technology. The purpose of this study was to mine the salt and alkali tolerance genes of millet and further explore the mechanism of salt and alkali tolerance of millet. We selected 18 representative samples and conducted in-depth sequencing using the latest sequencing platform to ensure the accuracy and reliability of the data.
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Project description:Abstract: In order to understand the expression patterns of miRNAs in alfalfa under alkali stress, small RNA sequencing was performed on alfalfa roots at different time points under alkali stress, and miRNAs were identified and analyzed.
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Project description:Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. Photosynthetic machinery is especially sensitive to saline-alkali stress. In addition, reversible protein phosphorylation also play crucial roles in plant salt resistance. While our knowledge on protein phosphorylation events in salt stress response is very limited. Few studies have been published involving photosynthetic protein phosphorylation modulation to improve salt resistance. In the present study, we investigated the Na2CO3-responsive characteristics in Puccinellia tenuiflora chloroplasts using stable isotope dimethyl labeled phosphoproteomic approach. A total of 161 unique phosphopeptides were identified, and 137 phosphopeptides were quantified by dimethyl labeling. Among them, 50 proteins were quantified as Na2CO3-responsive proteins with 57 phosphosites, including 33 increased and 14 decreased. Importantly, 26 phosphosites were newly identified as Na2CO3-responsive phosphoproteins in plants, which were supposed to be crucial for regulating photosynthesis, membrane and transporting, signaling, stress response, and protein synthesis and turnover. Among them, seven light harvesting proteins, six PSII proteins, five PSI proteins, three electron transfer chain proteins, and two Calvin cycle-related proteins were increased, but five ATP synthase subunits and sucrose-phosphate synthase were decreased at phosphorylation level. Besides, Na+/H+ antiporter, villin-2, and two thylakoid organization related proteins were increased at phosphorylation level. Two signaling related proteins and most protein species in charge of gene expression and protein turnover were enhanced at phosphorylation level at 24h after Na2CO3 treatment.
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2014-05-16 | E-GEOD-45724 | biostudies-arrayexpress
Project description:To investigate possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress than its recipient parental cultivar (Jijing88). By using microarray analysis, we examined global gene expression profiles in K83 and Jijing88, found more than 1,200 genes were constitutively differentially expressed in K83 compared with Jijing88, with 572 up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes in K83 were found up- and 156 down-regulated in K83, compared with 591 and 187 respectively in Jijing88.
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Project description:Alkali stress is an important means of inactivating undesirable pathogens in a wide range of situations, ranging from environmental cleaning of food processing environments, to the phagolysosomal killing of cells engulfed by mammalian phagocytes. Unfortunately, L. monocytogenes can launch an alkaline tolerance response (AlTR), significantly increasing persistence of the pathogen in such environments. This study compared the transcriptome patterns of alkali stressed and non alkali stressed L. monocytogenes 10403S cells, to elucidate the mechanisms by which this important pathogen adapts and/or grows during short or long-term alkali stress. Transcription profiles associated with alkali shock (AS) responses were obtained by DNA microarray analysis of mid-exponential cells suspended in pH 9 media for 15, 30 or 60 min. Transcription profiles associated with alkali adaptation (AA) were obtained by DNA microarray analysis of cells grown to mid-exponential phase in pH 9 media . Comparison of AS and AA transcription profiles with profiles from control (pH 7.0) cells identified over 2,000 genes that were differentially expressed under alkaline conditions. Rapid (15min) changes in expression included upregulation of genes encoding for multiple metabolic pathways, (including those associated with Na+/H+ antiporters), ABC transporters of functional compatible solutes such as carnitine, motility and virulence-associated genes as well as the σB controlled stress resistance network. Slower (30min and more) responses to AS and adaptation during growth in alkaline conditions (AA), included modest changes in mRNA concentrations, and genes involved in proton export. Keywords: Time course study of gene expression response to alkaline shock and adaptation
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