Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress
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ABSTRACT:
ORGANISM(S): Verbena bonariensis
PROVIDER: GSE113569 | GEO | 2019/04/24
REPOSITORIES: GEO
Similar Datasets
Project description:The samples were respectively from three replicates of the salt stress treatment and the control, then we obtained six cDNA libraries. In total, 983,827 transcripts and 469,059 unigenes were constructed. We got a total of 75,070 differentially expressed genes (DEGs), of which 48,965 were up-regulated and the other 26,105 were down regulated under the salt treatment.
2021-05-22 | GSE114752 | GEO
Project description:Cadmium (Cd)-contamination in soil has been becoming a major environmental problem in China. Ramie, a fiber crop, was frequently proposed to be used as the crop for phytoremediation of Cd-contaminated farmlands. However, high level Cd accumulation can cause a great inhibition of growth in ramie. To understand the potential mechanism for this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing in two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2) in this study. Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequencing reads generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, were De novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels between CO and CdS ramie revealed 155 differentially expressed genes (DEGs). Sixteen DEGs was further confirmed their expression difference by real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase which is a major enzyme for deactivating bioactive gibberellins (GAs) were found with a markedly up-regulated expression, which is possibly responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that a pathway (Cutin, suberine and wax biosynthesis) was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful for further understanding the mechanism of Cd-stressed response and improving the ability of Cd stress tolerance in ramie. A total of four samples, two replicates of control plants (CO1 and CO2) and two replicates of cadmium-stressed plants (CdS1 and CdS2) were used for RNA-seq.
2015-08-21 | E-GEOD-60583 | biostudies-arrayexpress
Project description:Cadmium (Cd)-contamination in soil has been becoming a major environmental problem in China. Ramie, a fiber crop, was frequently proposed to be used as the crop for phytoremediation of Cd-contaminated farmlands. However, high level Cd accumulation can cause a great inhibition of growth in ramie. To understand the potential mechanism for this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing in two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2) in this study. Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequencing reads generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, were De novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels between CO and CdS ramie revealed 155 differentially expressed genes (DEGs). Sixteen DEGs was further confirmed their expression difference by real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase which is a major enzyme for deactivating bioactive gibberellins (GAs) were found with a markedly up-regulated expression, which is possibly responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that a pathway (Cutin, suberine and wax biosynthesis) was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful for further understanding the mechanism of Cd-stressed response and improving the ability of Cd stress tolerance in ramie.
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Project description:Verbena bonariensis is a species with excellent garden plant, good environmental adaptability and great potential for future development.Cadmium has caused serious heavy metal pollution in the soil, which has posed a great threat to plant growth. In this study, Illumina sequencing technology was used to sequence the transcriptome of Verbena bonariensis leaf under normal and Cd stress, respectively. In total, 95,013 transcripts and 63021 genes with an average length of 923 bp and 1,246 bp were constructed from the clean sequence reads, respectively. And 1037 DEGs were found in response to cadmium treatment, of which 10 were selected for qRT-PCR. In conclusion, this study first identified the Verbena bonariensis as a heavy metal tolerant plant and provided the first large-scale transcriptional data set in response to cadmium stress. Our research will help to understand the mechanism of resistance to Cd in the Verbena bonariensis and provide clues for further studies on the relationships between plants and heavy metals in other Verbenaceae plants.
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Project description:To massively identify genes that are up-regulated by Cd and in particular transporter genes which might transport peptides or oligopeptides. Four week old hydroponically-grown Col-0 plants were treated with/without 200uM Cd for 6 hours. Total RNA was extracted from roots and subjected to hybridization with Affymetrix ATH1 microarrays.
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Project description:Heavy metal cadmium (Cd) affects seriously crop growth, quality and yield, and has potential threats to human safety. We found the difference of two ryegrasses (Lolium multiflorum Lam.), a high-Cd tolerance (LmHC) and a low-Cd tolerance (LmLC) cultivars , in response to cadmium stress. The germination rate, plant growth, and fresh weight of LmHC were much better than that of LmLC. So we use RNA sequencing to investigate the differentially expressed genes(DEGs) about cadmium response between LmHC and LmLC. Real-time quantitative PCR analysis showed that the same DEGs of LmLC and LmHC had obviously difference expression level under Cd treatment. It was suggestion that differential expression of DEGs might be involved in regulating Cd tolerance, accumulation and translocation.These results will be helpful for understanding the underlying molecular mechanism in Cd toxicity and provide references for improving the ecological environment through genetic improvement.
2020-01-30 | GSE144460 | GEO
Project description:The aim of this study is to do a side-by-side comparison of the transcriptomes that are regulated under Cu and Cd stress at the early stage in rice roots. The comparison of transcriptomes between Cu and Cd treatments and the application of bioinformatics procedures (e.g. regulated gene analysis) are potentially useful approaches for determining the both general and individual early responses triggered by each metal. Identify genes and pathways that would discriminate among the actions of Cu and Cd.
2016-01-22 | GSE34895 | GEO
Project description:To massively identify genes that are up-regulated by Cd and in particular transporter genes which might transport peptides or oligopeptides.
2010-06-04 | GSE22114 | GEO
Project description:Phytoremediation soil polluted by heavy metal has been drawn on a worldwide attention from human society. However, how to improve the efficiency of plant remediation of soil contaminated by cadmium remains unknown. Previous studies showed that nitrogen (N) significantly enhanced cadmium uptake in poplar plants. In order to further explore the key role of N in the detoxification against cadmium stress in plants, this study try to investigate the poplar proteome and phosphoproteome difference between Cd stress and Cd+N treatment. In total, 5838 of the 6573 identified were quantified. With a fold-change threshold >1.3 and p-value<0.05, 375 and 108 proteins were up- and down-regulated by Cd stress when compared to the control, 42 and 89 proteins were up- and down-regulated, respectively, in Cd+N / Cd group, 522 and 127 proteins were up- and down-regulated, respectively, in Cd+N / CK group. In addition, the phosphoproteome data was obtained after the proteomic difference was normalized, and 1471phosphosites in 721 proteins were quantified. Based on a fold-change threshold >1.2, P-value <0.05, the Cd stress up-regulated 8 phosphosites in 8 proteins and down-regulated 69 phosphosites in 58 proteins, whereas N+Cd treatment up-regulated 95 phosphosites in 86 proteins and down-regulated 17 phosphosites in 17 proteins when compared to sole Cd stress. In addition, N+Cd treatment up-regulated 74 phosphosites in 60 proteins and down-regulated 42 phosphosites in 37 proteins when compared to the control.Several putative responses to stress proteins, transcriptional and translational regulation factors were up-regulated by addition ofexogenous nitrogen followed Cd stress at the proteome and phosphoproteome levels. Especially, heat shock protein 70 (HSP70), peroxidase (POD), zinc finger protein (ZFP), ABC transporter protein (ABC), eukaryotic translation initiation factor (elF) and splicing factor 3B subunit 1-like (SF3BI) were up-regulated by Cd+N treatment whether at the proteome or at the phosphoproteome levels, which was need to further study. In a word, taken together of proteome and phosphoproteome data, nitrogen serves a protective role in plants treated with Cd by multiple ways.
2020-05-26 | PXD013360 | Pride
Project description:In this study, blueberry transcriptomics and rhizosphere fungal diversity were analyzed by simulated potting method to treat blueberries with Cd stress, and the content of Fe, Mn, Cu, Zn and Cd in each tissue, soil and DGT of blueberries were determined. , Combined with transcriptomics for correlation analysis. A total of 84374 annotated genes were obtained in blueberry roots, stems, leaves and fruits, of which 3370 DEGs were found, and DEGs in the stem accounted for the highest proportion, totaling 2521. The annotation results show that these DEGs are mainly concentrated in a series of metabolic pathways related to signal transduction, defense and pathogenic response. Blueberries transfer excess Cd from the root to the stem for storage. The stem contains the highest Cd content, which is consistent with the transcriptomics analysis results, while the fruit contains the lowest Cd content. Correlation analysis between heavy metal content and transcriptomics results in each tissue was carried out, and a series of genes related to Cd regulation were screened. The blueberry root system relies on mycorrhiza to absorb nutrients in the soil. The intervention of Cd has severely affected the microflora structure of the blueberry rhizosphere soil. Coniochaetaceae, which is extremely tolerant, has gradually become the dominant population.
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