Transcription profiling of Populus trichocarpa leaves in response to species diversity levels
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus trichocarpa
PROVIDER: E-MEXP-3910 | BioStudies |
REPOSITORIES: biostudies
Similar Datasets
Project description:Changes in gene expression in P. trichocarpa leaves was measured in response to growth competition by P. x canescens.Square petri dishes (12 x 12 cm) were filled autoclaved sand, 3 plantlets and Woody Plant Medium (WPM). In each petri dish we are growing 3 plantlets. As control 3 plantlets of P. trichocarpa and for the experiment a mixture of P. canescens and P. trichocarpa were P. trichocarpa is all the time the middle plantlet.
| E-MEXP-3909 | BioStudies
Project description:Changes in gene expression in P. trichocarpa leaves was measured in response to growth competition by P. x canescens.Square petri dishes (12 x 12 cm) were filled autoclaved sand, 3 plantlets and Woody Plant Medium (WPM). In each petri dish we are growing 3 plantlets. As control 3 plantlets of P. trichocarpa and for the experiment a mixture of P. canescens and P. trichocarpa were P. trichocarpa is all the time the middle plantlet.
2015-05-22 | E-MEXP-3909 | ArrayExpress
Project description:Changes in gene expression in P. trichocarpa leaves was measured in response to growth competition by P. x canescens.Square petri dishes (12 x 12 cm) were filled autoclaved sand, 3 plantlets and Woody Plant Medium (WPM). In each petri dish we are growing 3 plantlets. As control 3 plantlets of P. trichocarpa and for the experiment a mixture of P. canescens and P. trichocarpa were P. trichocarpa is all the time the middle plantlet.
2015-05-22 | E-MEXP-3910 | ArrayExpress
Project description:Populus × canescens plantlets were grown in Petri dishes on MS medium. 14 days old plantlets were co-incubated with L. bicolor without physical contact. After 2 and 7 days of co-incubation, roots and leaves were harvested.
| E-MTAB-8683 | BioStudies
Project description:Populus × canescens plantlets were grown in Petri dishes on MS medium. 14 days old plantlets were co-incubated with L. bicolor without physical contact. After 2 and 7 days of co-incubation, roots and leaves were harvested.
2020-12-10 | E-MTAB-8683 | ArrayExpress
Project description:Our analysis provides a comprehensive picture of how P. trichocarpa responds to drought stress at physiological and transcriptome levels which may help to understand molecular mechanisms associated with drought response and could be useful for genetic engineering of woody plants. Drought stress treatment was performed dividing P. trichocarpa plants into the well-watered (WW) group (soil volumetric water content of 40â45 %) and the water-limited group (soil volumetric water content of 10â15 %). Two cDNA libraries constructed separately from the WW and WL groups were subjected to high-throughput Illumina sequencing.
| E-MTAB-4126 | BioStudies
Project description:Plants harbor a diverse community of microbes, whose interactions with their host and each other can influence plant health and fitness. While microbiota in plant vegetative tissues has been extensively studied, less is known about members of the seed microbiota. We used culture-based surveys to identify bacteria and fungi found in the seeds of the model tree, <i>Populus trichocarpa</i>, collected from different sites. We found that individual <i>P. trichocarpa</i> seeds typically contained zero or one microbe, with common taxa including species of <i>Cladosporium</i>, <i>Aureobasidium</i>, <i>Diaporthe</i>, <i>Alternaria</i>, and <i>Pseudomonas,</i> a bacterium. <i>Pseudomonas</i> isolates were associated with seed mortality and were negatively associated with the occurrence of fungal isolates within <i>Epicoccum</i>, <i>Alternaria</i>, and <i>Aureobasidium</i> from the same seed. Next, we conducted an inoculation experiment with one of the isolated seed microbes, <i>Pseudomonas syringae pv. syringae</i>, and found that it reduced seed germination and increased seedling mortality for <i>P. trichocarpa</i>. Our findings highlight common fungi and bacteria in the seeds of <i>P. trichocarpa</i>, prompting further study of their functional consequences. Moreover, our study confirms that <i>P. syringae pv. syringae</i> is a seed pathogen of <i>P. trichocarpa</i> and is the first report that <i>P. syringae pv. syringae</i> is a lethal seedling pathogen of <i>P. trichocarpa</i>, allowing for future work on the pathogenicity of this bacterium in seedlings and potential antagonism with other seed microbes.
| S-EPMC8225106 | BioStudies
Project description:Populus deltoides and Populus trichocarpa were exposed to either ambient air or an acute ozone exposure of 200 ppb for 9 hrs and ozone response was profiled for each genotype by hybridising control against ozone-exposed samples per genotype. Keywords: stress response, genotype comparrison, ozone exposure RNA was extracted from the fifth leaf below the first fully unfurled leaf for each plant. Control and ozone-exposed plants were then randomly paired for hybridisation.
| E-GEOD-10874 | BioStudies
Project description:Populus trichocarpa is an important woody model organism whose entire genome has been sequenced. This resource has facilitated the annotation of microRNAs (miRNAs), which are short non-coding RNAs with critical regulatory functions. However, despite their developmental importance, P. trichocarpa miRNAs have yet to be annotated from numerous important tissues. Here we significantly expand the breadth of tissue sampling and sequencing depth for miRNA annotation in P. trichocarpa using high-throughput smallRNA (sRNA) sequencing. miRNA annotation was performed using three individual next-generation sRNA sequencing runs from separate leaves, xylem, and mechanically treated xylem, as well as a fourth run using a pooled sample containing vegetative apices, male flowers, female flowers, female apical buds, and male apical and lateral buds. A total of 276 miRNAs were identified from these datasets, including 155 previously unannotated miRNAs, most of which are P. trichocarpa specific. Importantly, we identified several xylem-enriched miRNAs predicted to target genes known to be important in secondary growth, including the critical reaction wood enzyme xyloglucan endo-transglycosylase/hydrolase and vascular-related transcription factors. This study provides a thorough genome-wide annotation of miRNAs in P. trichocarpa through deep sRNA sequencing from diverse tissue sets. Our data significantly expands the P. trichocarpa miRNA repertoire, which will facilitate a broad range of research in this major model system.
| S-EPMC3307732 | BioStudies
Project description:Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Here, we address fundamental questions regarding the molecular basis of adaptation in undomesticated forest tree populations to past climatic environments by employing an integrative quantitative genetics and landscape genomics approach. Using this comprehensive approach, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing QST-FST) using clustering of individuals by climate of origin (temperature and precipitation). 29,354 SNPs were investigated employing three different outlier detection methods and marker-inferred relatedness was estimated to obtain the narrow-sense estimate of population differentiation in wild populations. In addition, we compared our results with previously assessed selection of candidate SNPs using the 25 topographical units (drainages) across the P. trichocarpa sampling range as population groupings. Narrow-sense QST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant QST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees and we highlight that important loci underlying adaptive trait variation also show relationship to climate of origin. We consider our approach the most comprehensive, as it uncovers the molecular mechanisms of adaptation using multiple methods and tests. We also provide a detailed outline of the required analyses for studying adaptation to the environment in a population genomics context to better understand the species' potential adaptive capacity to future climatic scenarios.
| S-EPMC4658102 | BioStudies