Pinus massoniana
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ABSTRACT:
PROVIDER: PRJNA1019913 | ENA |
REPOSITORIES: ENA
Similar Datasets
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.
2018-01-18 | GSE101600 | GEO
Project description:The mechanisms of heavy metal accumulation in primary producers and the damage and stress response induced by heavy metals is not well understood. We used UHTS to analyze the transcriptomic response of Elodea nuttallii to heavy metal pollution. We exposed shoots of E. nuttallii for 24 h to increasing concentrations of Hg and Cd. Using Illumina RNA-Seq, we have generated over 50 million 54 nt paired end reads and 14 million single end reads, which we used for de novo assembly of the E. nuttallii transcriptome.
2012-02-01 | E-MTAB-892 | biostudies-arrayexpress
Project description:Heavy metal Zn pollution soil Metagenomic assembly
| PRJNA407391 | ENA
Project description:Transcriptional profiling of arsenic-induced toxicity and tolerance in Arabidopsis plants of different ecotypes Arsenic (As) is a toxic metalloid found ubiquitously in the environment and has widely been known as an acute poison and carcinogen. As toxicity is a major factor leading to root growth inhibition in plants. However, the molecular mechanisms of plants in response to As has not been extensively characterized. In this study, Arabidopsis ecotypes that are As-tolerant (Col-0) and -sensitive (Ws-2) were used to conduct a transcriptome analysis of the response to As (V). To begin elucidating the molecular basis of As toxicity and tolerance in Arabidopsis, seedlings of Col-0 and Ws-2 were subjected to As treatment. The root elongation rate of Col-0 was significantly higher than that of Ws-2 when exposed to As. The tolerant ecotype (Col-0) demonstrated lower accumulation of As when compared to the responses observed in the sensitive Ws-2. Subsequently, the effect of As exposure on genome-wide gene expression was examined in the two ecotypes. Comparative analysis of microarray data identified groups of genes with common and specific responses to As between Col-0 and Ws-2. The genes related to heat responses and oxidative stresses belonged to common responses, indicating conserved stress-associated changes across two ecotypes. The majority of specific responsive genes were those encoding heat shock proteins, heat shock factors, ubiquitin and transporters. The data suggested that metal transport and maintenance of protein structure may be important mechanisms for toxicity and tolerance to As. This study presents comprehensive surveys of global transcriptional regulation and identifies stress- and tolerance-associated genes in response to As.
2011-11-26 | GSE31977 | GEO
Project description:Environmental contamination from heavy metals poses a global concern for the marine environment, as heavy metals are passed up the food chain and persist in the environment long after the pollution source is contained. Cnidarians, dating back to 700 million years ago, play an important role in shaping marine ecosystems, but environmental pollution profoundly affects their vitality. Among the cnidarians, the sea anemone Nematostella vectensis is an advantageous model for addressing questions in molecular ecology and toxicology as it tolerates extreme environments and its genome has been published. Here we employed a transcriptome-wide RNA-Seq approach to analyze N.vectensis molecular defense mechanisms against four heavy metals: Hg, Cu, Cd and Zn. Altogether, more than 5000 transcripts showed significant changes in gene expression, with Hg having the greatest impact on up-regulating transcripts, followed by Cu, Cd and Zn. We identified, for the first time, co-up-regulation of immediate-early transcription factors such as Egr1, AP1 and NF-κB. Time-course analysis of these genes revealed their early expression as rapidly as one hour after exposure to heavy metals, suggesting that they may complement or substitute for the roles of the metal mediating Mtf1 transcripton factor. We further characterized regulation of a large array of stress-response gene families including Hsp, ABC, CYP members and phytochelatin synthase that may regulate synthesis of the metal-binding phytochelatins instead of the methallothioneins that are absent from Cnidaria genome. This study provides mechanistic insight into heavy-metal toxicity in N.vectensis and sheds light on ancestral stress adaptations. 4 metals were tested in triplicates in comparison to control (4 replicates)
2015-12-22 | E-GEOD-58769 | biostudies-arrayexpress
Project description:Transcriptional profiling of arsenic-induced toxicity and tolerance in Arabidopsis plants of different ecotypes Arsenic (As) is a toxic metalloid found ubiquitously in the environment and has widely been known as an acute poison and carcinogen. As toxicity is a major factor leading to root growth inhibition in plants. However, the molecular mechanisms of plants in response to As has not been extensively characterized. In this study, Arabidopsis ecotypes that are As-tolerant (Col-0) and -sensitive (Ws-2) were used to conduct a transcriptome analysis of the response to As (V). To begin elucidating the molecular basis of As toxicity and tolerance in Arabidopsis, seedlings of Col-0 and Ws-2 were subjected to As treatment. The root elongation rate of Col-0 was significantly higher than that of Ws-2 when exposed to As. The tolerant ecotype (Col-0) demonstrated lower accumulation of As when compared to the responses observed in the sensitive Ws-2. Subsequently, the effect of As exposure on genome-wide gene expression was examined in the two ecotypes. Comparative analysis of microarray data identified groups of genes with common and specific responses to As between Col-0 and Ws-2. The genes related to heat responses and oxidative stresses belonged to common responses, indicating conserved stress-associated changes across two ecotypes. The majority of specific responsive genes were those encoding heat shock proteins, heat shock factors, ubiquitin and transporters. The data suggested that metal transport and maintenance of protein structure may be important mechanisms for toxicity and tolerance to As. This study presents comprehensive surveys of global transcriptional regulation and identifies stress- and tolerance-associated genes in response to As. Comparison of Arabidopsis ecotype Col-0 and Ws-2 in response to As with the Affymetrix GeneChip were performed by the Affymetrix Gene Expression Service Lab (http://ipmb.sinica.edu.tw/affy/), supported by Academia Sinica, Taiwan
2011-11-26 | E-GEOD-31977 | biostudies-arrayexpress
Project description:Environmental contamination from heavy metals poses a global concern for the marine environment, as heavy metals are passed up the food chain and persist in the environment long after the pollution source is contained. Cnidarians, dating back to 700 million years ago, play an important role in shaping marine ecosystems, but environmental pollution profoundly affects their vitality. Among the cnidarians, the sea anemone Nematostella vectensis is an advantageous model for addressing questions in molecular ecology and toxicology as it tolerates extreme environments and its genome has been published. Here we employed a transcriptome-wide RNA-Seq approach to analyze N.vectensis molecular defense mechanisms against four heavy metals: Hg, Cu, Cd and Zn. Altogether, more than 5000 transcripts showed significant changes in gene expression, with Hg having the greatest impact on up-regulating transcripts, followed by Cu, Cd and Zn. We identified, for the first time, co-up-regulation of immediate-early transcription factors such as Egr1, AP1 and NF-κB. Time-course analysis of these genes revealed their early expression as rapidly as one hour after exposure to heavy metals, suggesting that they may complement or substitute for the roles of the metal mediating Mtf1 transcripton factor. We further characterized regulation of a large array of stress-response gene families including Hsp, ABC, CYP members and phytochelatin synthase that may regulate synthesis of the metal-binding phytochelatins instead of the methallothioneins that are absent from Cnidaria genome. This study provides mechanistic insight into heavy-metal toxicity in N.vectensis and sheds light on ancestral stress adaptations.
2015-12-22 | GSE58769 | GEO
Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients.
2014-07-22 | GSE59620 | GEO
Project description:Masson pine (Pinus massoniana) has evolved some adaptations for growth in low P soils. To elucidate these mechanisms, we investigated global gene expression profiles of the masson pine responding to long-term phosphorus starvation and different Pi levels (P1, 0.01 mM P; P2, 0.06 mM P).
2013-11-30 | GSE52835 | GEO
Project description:Genome sequencing and assembly
| PRJNA485122 | ENA