Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1117781 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29257211_1.fastq.gz | Fastqsanger.gz | |||
| SRR29257211_2.fastq.gz | Fastqsanger.gz | |||
| SRR29257212_1.fastq.gz | Fastqsanger.gz | |||
| SRR29257212_2.fastq.gz | Fastqsanger.gz | |||
| SRR29257213_1.fastq.gz | Fastqsanger.gz |
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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.
2018-07-06 | GSE98996 | GEO
Project description:Quinoa (Chenopodium quinoa) is a highly nutritious crop showing a remarkable tolerance to multiple abiotic stresses. The Catharanthus roseus RLK1-like kinase (CrRLK1L) family is involved in multiple processes during plant growth and stress responses. However, little is known about the members of the CqCrRLK1L subfamily and their biological functions. In this study, up to 26 CqCrRLK1L members were identified in quinoa genome. To systematically investigate their tissue-specific expression pattern and gene expression profiles in response to abiotic stresses, different quinoa samples including leaf, pistil, stamen, root, and leaf treated with NaCl were harvested for transcrioptome analysis with three biological replicates for each sample. Finally,we mapped about 30 million sequence reads per sample to the quinoa genome (NL-6) and combining the four different tissues (leaf, pistil, stamen, and root), totally 40382 genes were detected, accounting for 69% of total genes in quinoa. The expression of most CqCrRLK1Ls genes were detected in all four kind of tissues, and they showed tissue-specific expression pattern. In salt-treated leaves, we observe that about 6-thosands genes changed their expression, with log2FoldChange < -1 or >1 and p value <0.05. And four CqCrRLK1L genes largely altered their transcript levels, implying that these genes are involved in the regulation of salt stress response in quinoa. The present study provides a base for future research on elucidating the varied biological functions of CqCrRLK1Ls and their contributions to stress responses.
2022-06-27 | GSE198572 | GEO
Project description:Chenopodium quinoa, a pseudo-cereal and facultative halophyte, is a species of great economic potential. When exposed to saline soil, this salt-tolerant crop takes up sodium and chloride ions and sequesters large NaCl quantities in epidermal bladders cells (EBC). We have analyzed the Quinoa EBC transcriptome by RNA sequencing and elucidated the molecular identity and function of key ion transporters. Thereby we analyzed transcripts differentially expressed between EBCs and total leaves under control conditions.
2018-09-20 | E-MTAB-6112 | biostudies-arrayexpress
Project description:Soil salination and alkalization are global problems impairing plant survival by disrupting REDOX homeostasis. Whether melatonin regulates REDOX homeostasis at nitrosative level, and thus affects plant saline-alkali tolerance remains unknown. In saline-alkali stress, excess nitric oxide (NO) causes nitrosative damage in tomato roots. This NO can be degraded by S-nitrosoglutathione reductase (GSNOR), or stimulates caffeic acid O-methyltransferase (COMT) transcript for melatonin synthesis. Melatonin further feedback scavenges excess NO to alleviate nitrosative damage at the whole protein level, indicating by proteome S-nitrosylation. We target plasma membrane H+-ATPase 2 (HA2) and highlight that HA2 is S-nitrosylated at Cys206 in saline-alkali stress, reducing HA activity, H+ efflux, and tolerance by impairing its interaction with 14-3-3 protein 1 (TFT1). In agreement with these observations, COMT-mediated melatonin relieves the HA2 S-nitrosylation to recover its function and saline-alkali tolerance. Therefore, we propose NO and melatonin as a pair of REDOX switches to control HA2 S-nitrosylation and saline-alkali tolerance. Under natural saline-alkali conditions, tomato productivity can be improved by grafting with COMT-, GSNOR-, HA2-overexpression rootstocks or by genetic engineering non-nitrosylated HA2C206S mutants. Using melatonin-NO-HA2 module as a case, this study illuminates a novel molecular function of melatonin and relevant genetic engineering strategies in future agriculture.
2025-04-28 | PXD056815 | Pride
Project description:Alkali stress is an important limiting factor for agricultural production. The aim of this study was to investigate whether old and young leaves have different biochemical responses to alkali stress in hexaploid wheat, and to provide molecular dissection of these differential responses on the basis of proteomic profiling. Under alkali stress, hexaploid wheat accumulated higher concentrations of Na+ in older leaves to protect young leaves. Young leaves accumulated amino acids, carbohydrates, and dehydrin proteins to relieve Na+ toxicity. Under alkali stress, 14-3-3 protein abundance was enhanced in old leaves to accelerate Na+ compartmentation in the vacuole. Abundances of 27 ribosomal proteins were significantly decreased in old leaves but not in young leaves, and many proteinases and ribonucleases also were significantly upregulated by alkali stress in old leaves. Interestingly, one E3 ubiquitin-protein ligase, one ubiquitin protein, and one proteasome protein were simultaneously upregulated in old leaves but not in young leaves. We propose that during the response to alkali stress, old leaves may programmatically degrade ribosomes through the ubiquitin-proteasome pathway to generate amino acids, which will increase tissue tolerance. Alkali stress induced remarkable enhancement of almost all free amino acids and ribose contents in old leaves, thus supporting this hypothesis. In addition, we observed that, for some salinity-tolerant protein-triads, the A, B, and D homoeologous proteins showed different response to alkali stress. This suggests that alkali stress may influence the translation of homoeologous genes, resulting in imbalanced translation of A, B, and D homoeologous genes in some gene triads.
2019-11-20 | PXD016354 |
Project description:Purpose:Salinity is an important environmental factor that affects the physiological activities of fish. The goals of this study are investigating the effect of different saline-alkali stress on grass carp (Ctenopharyngodon idella). Methods: Grass carp individuals, averaging 12 cm in body length, were obtained from Duofu fish farm (Wuhan, China) and cultured at recirculating aquaculture system for 2 weeks before the experiment began. For the challenge, all grass carp were randomly divided into three groups, and then cultured at saline-alkali water with the concentration of 0, 3‰ and 6‰. After 30 days, some grass crap cultured at 3‰ and 6‰ saline-alkali water were injured. At the same time, gill samples of grass carp were collected from 0, 3‰ (grass carp was not injured), 3‰ (grass carp was injured), 6‰ (grass carp was not injured) and 6‰ (grass carp was injured)saline-alkali groups. Total RNA of all samples was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's introduction. RNA integrity was assessed using an Agilent 2100 bioanalyzer (Agilent, USA). Samples with RNA integrity numbers (RINs) ≥ 7.5 were subjected to cDNA library construction using TruseqTM RNA sample prep Kit (Illumina). Results:A total of 15 were processed for transcriptome sequencing, generating 94.99Gb Clean Data. At least 5.76Gb clean data were generated for each sample with minimum 91.87% of clean data achieved quality score of Q30. Clean reads of each sample were mapped to specified reference genome. Mapping ratio ranged from 88.59% to 92.84%. The expression of genes was quantified and differentially expressed genes were identified based on their expression.Criteria for differentially expressed genes was set as Fold Change(FC)≥1.5 and Pvalue<0.05. Fold change(FC) refers to the ratio of gene expression in two samples. These DEGs were further processed for functional annotation and enrichment analysis. Conclusions: Our study represents Effects and molecular regulation mechanisms of saline-alkali stress on the healthy grass carp by using RNA-seqtechnology. Our results show that saline-alkali stress will impair the immune system of grass carp.
2021-12-31 | GSE185170 | GEO
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.
2021-12-15 | GSE190890 | GEO