Ceriops tagal
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA348664 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4454162.fastq.gz | Fastqsanger.gz | |||
| SRR4470215.fastq.gz | Fastqsanger.gz | |||
| SRR4470216.fastq.gz | Fastqsanger.gz | |||
| SRR4470476.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Time course profiles in salt shock roots of Ceriops tagal
| PRJNA146319 | ENA
Project description:Transcriptional differentiation in response to environmental stresses plays critical roles in adaptation. Mangroves are dominant in intertidal zones and form dense forest at the sea-land interface, but little is known about the impact of transcriptional phenotype on their adaptation to the saline environments. To address this issue, we prepared customized chips containing cDNA from the root cDNA library of a mangrove species, Ceriops tagal, and then monitored the time-course transcript profiles in the roots by conducting a series of microarray experiments. Five durations of salt shock with 500 mM NaCl, namely 2, 5, 10, 24 and 192 hours, were included. A total of 88 unigenes that were recognized to be up- or down-regulated by salt shock and both gene categories in relation to stresses-induced responses and transcription factor activity were over-predominant. The stresses-responsive genes were significantly overrepresented, some of which were regulated in differential manners from their homologues genes in Arabidopsis. Specific transcriptional regulations were employed by C. tagal to cope with salt shock, which could benefit the salt-tolerant lifestyle of this mangrove species and possibly contribute to establishment of adaptation to the saline environments.
2013-12-31 | GSE30909 | GEO
Project description:Ceriops tagal isolate:CT-1 Genome sequencing and assembly
| PRJNA698757 | ENA
Project description:Transcriptional differentiation in response to environmental stresses plays critical roles in adaptation. Mangroves are dominant in intertidal zones and form dense forest at the sea-land interface, but little is known about the impact of transcriptional phenotype on their adaptation to the saline environments. To address this issue, we prepared customized chips containing cDNA from the root cDNA library of a mangrove species, Ceriops tagal, and then monitored the time-course transcript profiles in the roots by conducting a series of microarray experiments. Five durations of salt shock with 500 mM NaCl, namely 2, 5, 10, 24 and 192 hours, were included. A total of 88 unigenes that were recognized to be up- or down-regulated by salt shock and both gene categories in relation to stresses-induced responses and transcription factor activity were over-predominant. The stresses-responsive genes were significantly overrepresented, some of which were regulated in differential manners from their homologues genes in Arabidopsis. Specific transcriptional regulations were employed by C. tagal to cope with salt shock, which could benefit the salt-tolerant lifestyle of this mangrove species and possibly contribute to establishment of adaptation to the saline environments. A reference design was used to analyze gene expression differences. Salt stressed young roots were harvested from seedlings of C. tagal at the ends of each shock duration. Young roots of unshocked seedlings were used as controls and harvested at the same time. Three biological replicates were set up for each treatment and corresponding control, respectively, each containing a pool of total RNA from 4 seedlings. Salt stressed samples were compared with the corresponding controls at each time point by co-hybridizing to the customized cDNA arrays
2013-12-31 | E-GEOD-30909 | biostudies-arrayexpress
Project description:Identification of genes involved in mangrove species' adaptation to salt stress can provide valuable information for developing salt-tolerant crops and understanding the molecular evolution of salt tolerance in halophiles. Ceriops tagal is a salt-tolerant mangrove tree growing in mudflats and marshes in tropical and subtropical areas, without any prior genome information. In this study, we assessed the biochemical and transcriptional responses of C. tagal to high salt treatment (500 mmol/L NaCl) by hydroponic experiments and RNA-seq. In C. tagal root tissues under salt stress, proline accumulated strongly from 3 to 12 h of treatment; meanwhile, malondialdehyde content progressively increased from 0 to 9 h, then dropped to lower than control levels by 24 h. These implied that C. tagal plants could survive salt stress through biochemical modification. Using the Illumina sequencing platform, approximately 27.39 million RNA-seq reads were obtained from three salt-treated and control (untreated) root samples. These reads were assembled into 47,111 transcripts with an average length of 514 bp and an N50 of 632 bp. Approximately 78% of the transcripts were annotated, and a total of 437 genes were putative transcription factors. Digital gene expression analysis was conducted by comparing transcripts from the untreated control to the three salt treated samples, and 7,330 differentially expressed transcripts were identified. Using k-means clustering, these transcripts were divided into six clusters that differed in their expression patterns across four treatment time points. The genes identified as being up- or downregulated are involved in salt stress responses, signal transduction, and DNA repair. Our study shows the main adaptive pathway of C. tagal in saline environments, under short-term and long-term treatments of salt stress. This provides vital clues as to which genes may be candidates for breeding salt-tolerant crops and clarifying molecular mechanisms of salt tolerance in C. tagal. The expression levels of 20 candidate genes measured by RNA-Seq were validated via qRT-PCR. Eighteen genes showed consistent expression patterns in RNA-Seq and qRT-PCR results, suggesting that the RNA-seq dataset was dependable for gene expression pattern analysis.
| S-EPMC5147905 | biostudies-literature
Project description:IntroductionCeriops decandra (CD) and Ceriops tagal (CT) are two traditionally used mangrove plants widely distributed along the coastal areas of South Asia, Africa, South Pacific. In this study, we evaluated the diuretic potential of aerial roots of CD, CT and assessed the effectiveness of the plants' terpenoids enriched bioactive constituents against human carbonic anhydrase (hCA) enzyme through molecular docking.Materials and methodsFirstly, the acute toxicity of CD and CT was evaluated in mice. In vivo diuretic activity was then studied in mice and the volume of excreted urine was measured. The urine was further examined for pH, density and Na+, K+, Cl- concentrations. From this, the saluretic, natriuretic, kaliuretic and CAI (carbonic anhydrase inhibitory) activities were calculated. Finally, total terpenoid contents (TTC) of the plant extracts were quantified and the terpenoids previously reported from both CD and CT were docked against four hCA isoforms - hCAII, hCAIV, hCAXII and hCAXIV.ResultsIn the acute toxicity assessment, no sign of toxicity was found. In diuretic activity evaluation, both extracts displayed substantial increase in urine volume, with CD being at top. Concentrations of Na+, K+ and Cl- were also upsurged at a high dose of treatment (500 mg/kg). Both extracts at 500 mg/kg dose demonstrated potent saluretic, natriuretic and CAI activity. The TTC of CD was significantly higher than CT. In molecular docking analysis, greater binding affinity against hCA isoforms was demonstrated by the terpenoids reported from CD.ConclusionAerial roots of both CD and CT possess substantial diuretic activity with an inhibitory effect on CA. Here, diuretic potential as well as the total terpenoid content of CD were much greater between the two.
| S-EPMC8318864 | biostudies-literature