RNA-seq analysis of date-palms treated with stress hormone ABA compared to controls
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 1000
ORGANISM(S): Phoenix dactylifera
SUBMITTER: Thomas Nussbaumer
PROVIDER: E-MTAB-5261 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Purpose: To identify conserved and novel miRNAs in date palm and, most importantly, to identify miRNAs that could play a role in salt tolerance Methods: we generated sRNA libraries from the leaves and roots of NaCl-treated and untreated seedlings of date palm,then Deep sequencing of these four sRNA libraries,last The bioinformatics analysis,further validated using semi-quantitative PCR (qPCR). Results: Deep sequencing of these four sRNA libraries yielded approximately 251 million reads. The bioinformatics analysis has identified 153 homologs of conserved miRNAs, 89 miRNA variants, and 180 putative novel miRNAs in date palm. Expression profiles under salinity revealed differential regulation of most miRNAs in date palm. In leaves, all of the identified miRNAs were affected by the salinity treatment, and the majority (75%) of them were upregulated, whereas in roots, only 33% of the miRNAs were upregulated, but 44% of them were downregulated, while the remaining miRNAs (22%) were unaffected by the treatment. The salt responsiveness of some of these miRNAs was further validated using semi-quantitative PCR (qPCR). Some of the predicted targets for the identified miRNA include genes with known functions in plant salt tolerance, such as potassium channel AKT2-like proteins, vacuolar protein sorting-associated protein, and calcium-dependent and mitogen-activated proteins. As one of the first cultivated trees in the world with a wide range of abiotic stress tolerance, date palm contains a large population of conserved and nonconserved miRNAs that function at the posttranscriptional level. Conclusions: This study provided insights into miRNA-mediated gene expression that are important for adaptation to salinity in date palms.
2016-12-31 | GSE71445 | GEO
Project description:Climate change is increasing the frequency and intensity of warming and drought periods around the globe, currently representing a threat to many plant species. Understanding the resistance and resilience of plants to climate change is, therefore, urgently needed. As date palm (Phoenix dactylifera) evolved adaptation mechanisms to a xeric environment and is able to tolerate large diurnal and seasonal temperature fluctuations, we studied the protein expression changes in their leaves, volatile organic compound emissions, and photosynthesis in response to variable growth temperatures and soil water deprivation. Plants were grown under controlled environmental conditions under simulated Saudi Arabian summer and winter climates followed by drought stress. We show that date palm is able to counteract the harsh conditions of the Arabian Peninsula by adjusting the abundances of proteins related to the photosynthetic machinery, abiotic stress and secondary metabolism. Under summer climate and water deprivation, these adjustments included efficient protein expression response mediated by heat shock proteins and the antioxidant system to counteract reactive oxygen species formation. Proteins related to secondary metabolism were downregulated, except for the P. dactylifera isoprene synthase (PdIspS), which was strongly upregulated in response to summer climate and drought. This study reports for the first time, the identification and functional characterization of the gene encoding for PdIspS, allowing future analysis of isoprene functions in date palm under extreme environments. Overall, the current results show that protein reprogramming of date palm leaves contribute to heat and drought tolerance. We conclude that the protein plasticity of date palm is one important mechanism of molecular adaptation to remarkable environmental fluctuations.
2022-02-16 | PXD021666 | Pride
Project description:RNA-seq analysis of date-palms treated with stress hormone ABA compared to controls
| PRJEB18007 | ENA
Project description:Two tissues (root and shoot) of a salt tolerant (Khalas) and a salt sensitive (Nabut Saif) variety of date palm (Phoenix dactylifera) were salt treated and compared to control conditions by RNAseq.
2023-12-31 | E-MTAB-11001 | biostudies-arrayexpress
Project description:The aim of this experiment is to understand the impact of overexpression of ERD15 on the transcriptome of Arabidopsis thaliana. ERD15 was isolated from a screen for genes rapidly induced after pathogen treatment from Arabidopsis. This gene was originally found as early responsive to drought (Kiyosue et al., 1994, Plant Physiol 106, 1707). ABA is central phytohormone in drought response, but increasing information is pointing to its significant role in pathogen responses as well. We are interested to see the effect of this hormone on plants overexpressing ERD15 compared to control plants. The samples (rosette leaves)will be harvested from 3-week old soil grown plants 90 min after spraying with 100 micromolar ABA. Comparison will be made with non-treated plant samples. Experimenter name = Elina Helenius; Experimenter phone = +358 9 191 59085; Experimenter fax = +358 9 191 59079; Experimenter institute = University of Helsinki; Experimenter address = Viikinkaari 5 D; Experimenter address = P.O.Box 56; Experimenter address = Helsinki; Experimenter zip/postal_code = 00014; Experimenter country = Finland Experiment Overall Design: 4 samples were used in this experiment
2008-06-13 | E-GEOD-5521 | biostudies-arrayexpress
Project description:Heterotrimeric G proteins mediate crucial and diverse signaling pathways in eukaryotes. To gain insights into the regulatory modes of the G protein and the co-regulatory modes of the G protein and the stress hormone abscisic acid (ABA), we generated and analyzed gene expression in G protein subunit single and double mutants of the model plant Arabidopsis thaliana. Through a Boolean modeling approach, our analysis reveals novel modes of heterotrimeric G protein action. Keywords: transcriptome analysis; G protein subunit mutants; abscisic acid (ABA) Microarray data were generated from four genotypes (wild type, gpa1-4 mutant, agb1-2 mutant, agb1-2 gpa1-4 double mutant) with or without ABA treatment. Arabidopsis plants were grown in growth chambers with an 8 hr light/16hr dark. Three hundred Arabidopsis leaves excised from 60-70 five-week-old plants were used as the starting material for each guard cell microarray. Ten mature leaves taken from 3-4 plants grown side-by side with the plants for guard cell isolation were used for each leaf sample. Excised leaf and isolated guard cell samples were treated with ABA (50 μM) or EtOH (solvent control) for 3 hrs. For each type of sample (guard cells or leaves), three independent biological replicates were performed, resulting in a total of 48 microarray hybridizations (2 sample types ´ 4 genotypes ´ two treatments ´3 replicates).
2010-12-06 | E-GEOD-19520 | biostudies-arrayexpress
Project description:Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. We studied in parallel microRNA profiles on the same samples and we will try to identify sunflower microRNA regulated genes in response to ABA. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.-The experiment consisted of 3 repeats of four 12-day-old-plantlets of sunflower genotype SF193 (INRA code: XRQ) grown in growth chamber conditions and submitted to a 6-hour-treatment of 10 µM absissic acid or not. Growth conditions were 14h light at 23°C and 10h night at 20°C under fluorescent bulbs. Plants were grown in 6 hydroponic boxes containing 20 litres of aerated liquid culture medium (as described in Massonneau et al., 2001 Planta). Leaves (not cotyledons) 1 to 4 were harvested 4 hours after light onset and frozen immediately in liquid nitrogen. 6 arrays - SUNFLOWER; treated vs untreated comparison
2012-12-09 | E-GEOD-22519 | biostudies-arrayexpress
Project description:Purpose: to screen the candidate genes involved in the peanut drought stress response, we conducted global transcriptome analysis of peanut plants challenged with water deficit and ABA, using the Illumina HiSeq2000 sequencing platform. Methods: a sequences library of Yueyou7 were constructed at first. Then the profile of diffentialy expressed genes (DEGs) under three different treatments (control, water deficit without ABA, and water deficit with ABA) were conducted based on above sequence library. For sequencing library construction, plants were grown under normal conditions, as described previously , Seeds were planted in soil and kep in the greenhouse at temperature of 25-30M-bM-^DM-^C and water well. Three tissues (leaves, roots, and stems) were collected at three development stages (four-leaf, flowering and podding stages), respectively. Then all of these tissues were mixed to extract the total RNA for sequence library construction. For DEGs study, two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 M-BM-5mol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel. After treatments, Total RNA was extracted from 100 mg of plant material, and RNA integrity was checked by gel electrophoresis. Also RNA quality was checked and RNA was quantified using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA) and Nanodrop ND-1000 (Thermo Scientific, Waltham, USA). Results: we generated 4.96M-CM-^W107 raw sequence reads and assembled the high quality reads into 92,390 unique genes. Compared with the control, we found that 621 genes (M-bM-^IM-%1.5 fold change) responded rapidly to water deficit and 2665 genes (M-bM-^IM-%1.5 fold change) responded rapidly to ABA. We found 279 genes that overlapped between water deficit and ABA responses, 264 genes that showed the same trend in expression while 15 genes expression that showed opposite trend. Among the identified genes, 257 showed high induction by ABA (>5 fold), and 19 showed high induction by drought (>5 fold). In addition, we identified 100 transcription factor genes among the ABA-inducible genes but only 22 transcription factor genes among the water deficit-inducible genes. Conclusions: we identified genes differentially expressed in the early response to water deficit or ABA. These genes were annotated with GO functional categories for water deficit (33 categories) or ABA (31 categories). We found that only 19 genes were highly induced by water deficit, but 257 genes were highly induced by ABA. Our previous work has examined many of these genes and our future work will reveal their functions and relationships. These data will facilitate functional genomic studies and have established a biotechnological platform for examination of the early drought- and ABA-responsive transcriptome regulatory network in peanut. Two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 M-BM-5mol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel.
2014-05-13 | E-GEOD-56439 | biostudies-arrayexpress
Project description:Background: Abscisic acid (ABA) regulates various developmental processes and stress responses over both short (i.e. hours or days) and longer (i.e. months or seasons) time frames. To elucidate the transcriptional regulation of early responses of grapevine (Vitis vinifera) responding to ABA, different organs of grape (berries, shoot tips, leaves, roots and cell cultures) were treated with 10 μM (S)-(+)-ABA for 2 h. NimbleGen whole genome microarrays of Vitis vinifera were used to determine the effects of ABA on organ-specific mRNA expression patterns. Results: Transcriptomic analysis revealed 839 genes whose transcript abundances varied significantly in a specific organ in response to ABA treatment. No single gene exhibited the same changes in transcript abundance across all organs in response to ABA. The biochemical pathways affected by ABA were identified using the Cytoscape program with the BiNGO plug-in software. The results indicated that these 839 genes were involved in several biological processes such as flavonoid metabolism, response to reactive oxygen species, response to light, and response to temperature stimulus. ABA affected ion and water transporters, particularly in the root. The protein amino acid phosphorylation process was significantly overrepresented in shoot tips and roots treated with ABA. ABA affected mRNA abundance of genes (CYP707As, UGTs, and PP2Cs) associated with ABA degradation, conjugation, and the ABA signaling pathway. ABA also significantly affected the expression of several transcription factors (e.g. AP2/ERF, MYC/MYB, and bZIP/AREB). The greatest number of significantly differentially expressed genes was observed in the roots followed by cell cultures, leaves, berries, and shoot tips, respectively. Each organ had a unique set of gene responses to ABA. Conclusions: This study examined the short-term effects of ABA on different organs of grapevine. The responses of each organ were unique indicating that ABA signaling varies with the organ. Understanding the ABA responses in an organ-specific manner is crucial to fully understand hormone action and plant responses to water deficit. Shoot tips and berries samples were collected at the University of California, Davis, CA, USA (2010); cell culture samples were sampled at Oregon State University, OR, USA (2010); roots and leaf samples were collected at the University of Nevada, Reno, Reno, NV, USA (2011). Three independent experimental (and biological) replicates were harvested to compare between ABA-treated and untreated samples. Tissue was derived from Vitis vinifera L. cv. Cabernet Sauvignon.
2016-03-01 | E-GEOD-78798 | biostudies-arrayexpress
Project description:In this project, leaves and EBCs of the halophyte plant Chenopodium quinoa were treated with ABA. The effect of the ABA treatment was analyzed by comparing to non-treated leaves and EBCs.
2022-05-10 | E-MTAB-10419 | biostudies-arrayexpress