Arabidopsis thaliana
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR217257_1.fastq.gz | Fastqsanger.gz | |||
| DRR217257_2.fastq.gz | Fastqsanger.gz | |||
| DRR217258_1.fastq.gz | Fastqsanger.gz | |||
| DRR217258_2.fastq.gz | Fastqsanger.gz | |||
| DRR217259_1.fastq.gz | Fastqsanger.gz |
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Project description:Comparative genomics between enophytic and pathogenic Colletotrichum species isolated from field-grown healthy Brassicaceae plants
| PRJDB9370 | ENA
Project description:Background: Thellungiella salsuginea is an important model plant due to its natural tolerance to abiotic stresses including salt, cold, and water deficits. Microarray and metabolite profiling have shown that Thellungiella undergoes stress-responsive changes in transcript and organic solute abundance when grown under controlled environmental conditions. However, few reports assess the capacity of plants to display stress-responsive traits in natural habitats where concurrent stresses are the norm. Results: To determine whether stress-responsive changes observed in cabinet-grown plants are recapitulated in the field, we analyzed leaf transcript and metabolic profiles of Thellungiella growing in its native Yukon habitat during two years of contrasting meteorological conditions. We found 673 genes showing differential expression between field and unstressed, chamber-grown plants. There were comparatively few overlaps between genes expressed under field and cabinet treatment-specific conditions. Only 20 of 99 drought-responsive genes were expressed both in the field during a year of low precipitation and in plants subjected to drought treatments in cabinets. There was also a general pattern of lower abundance among metabolites found in field plants relative to control or stress-treated plants in growth cabinets. Nutrient availability may explain some of the observed differences. For example, proline accumulated to high levels in cold and salt-stressed cabinet-grown plants but proline content was, by comparison, negligible in plants at a saline Yukon field site. We show that proline accumulated in a stress-responsive manner in Thellungiella plants salinized in growth cabinets and in salt-stressed seedlings when nitrogen was provided at 1.0 mM. In seedlings grown on 0.1 mM nitrogen medium, the proline content was low while carbohydrates increased. The relatively higher content of sugar-like compounds in field plants and seedlings on low nitrogen media suggests that Thellungiella shows metabolic plasticity in response to environmental stress and that resource availability can influence the expression of stress tolerance traits under field conditions. Conclusion: Comparisons between Thellungiella plants responding to stress in cabinets and in their natural habitats showed differences but also overlap between transcript and metabolite profiles. The traits in common offer potential targets for improving crops that must respond appropriately to multiple, concurrent stresses.
2012-10-22 | GSE41182 | GEO
Project description:The objective of this study was on the one hand to compare the transcriptional dynamics of mutualistic Colletotrichum tofieldiae and pathogenic Colletotrichum incanum during colonization of Arabidopsis roots and on the other hand also examine the corresponding host responses Arabidopsis seeds that were either untreated (mock) or inoculated with Colletotrichum tofieldiae (isolate 0861) or Colletotrichum incanum (isolate MAFF230704) were grown in normal (P+) or low (P-) phosphate conditions. Roots (with/without fungal colonization) were collected at 6, 10, 16, and 24 days post inoculation (dpi). Additionally, C. tofieldiae and C. incanum in vitro hyphae were collected after two days growth in liquid Mathurâs medium. For each condition three replicates were obtained.
2016-03-17 | E-GEOD-70094 | biostudies-arrayexpress
Project description:Background: The investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions. Accordingly, transcriptome sequencing offers a powerful approach to address questions concerning the influence of natural habitat on the physiology of an organism. We used RNA sequencing of Eutrema salsuginuem, an extremophile relative of Arabidopsis thaliana, to investigate the extent to which genetic variation and controlled versus natural environments contribute to differences between transcript profiles. Results: Using 10 million cDNA reads, we compared transcriptomes from two natural Eutrema accessions (originating from Yukon Territory, Canada and Shandong Province, China) grown under controlled conditions in cabinets and those from Yukon plants collected at a Yukon field site. We assessed the genetic heterogeneity between individuals using single-nucleotide polymorphisms (SNPs) and the expression patterns of 27,016 genes. Over 39,000 SNPs distinguish the Yukon from the Shandong accessions but only 4,475 SNPs differentiated transcriptomes of Yukon field plants from an inbred Yukon line. We found 2,898 genes that were differentially expressed between the three sample groups and multivariate statistical analyses showed that transcriptomes of individual plants from a Yukon field site were as reproducible as those from inbred plants grown under controlled conditions. Predicted functions based upon gene ontology classifications show that the transcriptomes of field plants were enriched by the differential expression of light- and stress-related genes, an observation consistent with the habitat where the plants were found. Conclusion: Our expectation that comparative RNA-Seq analysis of transcriptomes from plants originating in natural habitats would be confounded by uncontrolled genetic and environmental factors was not borne out. Moreover, the transcriptome data shows little genetic variation between laboratory Yukon Eutrema plants and those found at a field site. Transcriptomes were reproducible and biological associations meaningful whether plants were grown in cabinets or found in the field. Thus RNA-Seq is a valuable approach to study native plants in natural environments and this technology can be exploited to discover new gene targets for improved crop performance under adverse conditions. Funding Acknowledgement: This work was sponsored by an Ontario Research Fund-Research Excellence award 03-043 to EAW and RKC with support from by Viterra Inc. and Sigma-Aldrich.
2013-08-30 | GSE49378 | GEO
Project description:Transcriptional changes in field-grown plants of Vitis Vinifera cultivars 'Chardonnay' and 'Incrocio Manzoni' naturally infected with Bois Noir phytoplasma, compared to healthy samples. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Nicola Pecchioni. The equivalent experiment is VV14 at PLEXdb.]
2009-09-09 | GSE12842 | GEO
Project description:Pseudomonas strains isolated from the rhizosphere and phyllosphere of field-grown potato plants
| PRJNA355625 | ENA
Project description:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. To identify heat stress induced genes, we performed RNA-sequencing of rosette leaves from mock-treated, heat-stressed and heat-stressed-recoved plants of both species.
2015-08-01 | GSE69077 | GEO
Project description:Nicotiana benthamiana plants were grown to the 8th true leaf development stage with 16 h light at 150 mol s-1 m-2 with 25/17oC day/night temperatures. Colletotrichum orbiculare strain ATCC20767 and Pseudomonas syringae pv. tabaci strain BPIC4 was grown in pure cultures to obtain syringae pv. tabaci strain BPIC4 was grown in pure cultures to obtain conidia and cells, respectively. Leaves of N. benthamiana plants were inoculated by spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare as described by Shen et al. (2001) or by infiltrating with a needle-less syringe 2 X 105 CFU/ml in sterile 10 mM MgCl2 for P. syringae pv. tabaci according to Rommens et al. (1995). For a control, healthy leaves were sprayed with sterile H2O or infiltrated with sterile 10 mM MgCl2 and then incubated under the same conditions for the same period of time as the pathogen-inoculated plants. Total RNA was extracted at 12 hours and 1, 2, 3 and 4 days after inoculation. The first and second mature leaf was excised and immediately frozen at -70 C. Keywords: Direct comparison
2007-09-01 | GSE8211 | GEO
Project description:The objective of this study was on the one hand to compare the transcriptional dynamics of mutualistic Colletotrichum tofieldiae and pathogenic Colletotrichum incanum during colonization of Arabidopsis roots and on the other hand also examine the corresponding host responses
2016-03-17 | GSE70094 | GEO
Project description:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. lyrata that allow for intra-specific transcriptome comparison in several major developmental stages. Arabidopsis lyrata and Arabidopsis thaliana aerial tissues were collected from mock treated plants, total RNA isolated and poly-A RNA populations sequenced
2015-08-01 | E-GEOD-69222 | biostudies-arrayexpress