Panicum sp. cultivar:Panicum
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ABSTRACT:
PROVIDER: PRJNA705527 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Panicum virgatum tissues (including leaves, drought-treated leaves and flowers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, drought-treated leaves and flowers of Panicum virgatum. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Pamela Green for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
2011-05-09 | E-GEOD-28980 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Panicum virgatum tissues (including leaves, drought-treated leaves and flowers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
2011-05-10 | GSE28980 | GEO
Project description:Cereal aphids can successfully colonize and damage switchgrass (Panicum virgatum) plants. Among the aphids tested, greenbugs (Schizaphis graminum, GB) caused significant plant damage likely through a combination of aphid-salivary proteins that are injected into plants during feeding and a strong host response elicited by herbivory. In this study, changes in protein phosphorylation present in GB-infested and uninfested control plants was determined. These data were compared against transcriptome changes recently published for this system.
2022-02-04 | PXD018546 | Pride
Project description:Cereal aphids can successfully colonize and damage switchgrass (Panicum virgatum) plants. Among the aphids tested, greenbugs (Schizaphis graminum, GB) caused significant plant damage likely through a combination of aphid-salivary proteins that are injected into plants during feeding and a strong host response elicited by herbivory. In this study, shotgun label-free proteomics has been used to document changes to the switchgrass proteome as a result of GB infestation. These proteomic data were compared against transcriptome changes recently published for this system.
2022-02-04 | PXD018547 | Pride
Project description:Sustainable production of switchgrass (Panicum virgatum) as a bioenergy crop hinges in part on efficient use of soil macronutrients, especially nitrogen (N). This study investigated the physiological, metabolic and transcriptomic responses of switchgrass to N limitation. Moderate N limitation marked a tipping point for large changes in plant growth, root-to-shoot ratio, root system architecture and total nitrogen content. Integration of transcriptomic and metabolic data revealed that N limitation reduced switchgrass photosynthetic capacity and carbon(C)-fixation activities. Switchgrass balanced C-fixation with N-assimilation, transport and recycling of N compounds by rerouting C-flux from glycolysis, the oxidative branch of the pentose phosphate pathway (OPPP) and from the tricarboxylic acid (TCA) cycle in an organ specific manner. The energy and reduction power so generated, and C-skeletons appear to be directed towards N uptake, biosynthesis of energy storage compounds with high C/N ratio such as sucrose, non-N-containing lipids, and various branches of secondary metabolism.
2023-12-31 | GSE237286 | GEO
Project description:H. seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize and promote plant growth wheat seedlings growing hydroponically in Hoaglandâs medium were inoculated with H. seropedicae the bacteria and incubated for 3 days. mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of bacteria attached to the root and planktonic revealed an extensive metabolic adaptation to the epiphytic life style.
2016-07-03 | E-MTAB-3646 | biostudies-arrayexpress
Project description:Penicillium meliponae, a recently described and rare species, was isolated as an endophytic fungus from the Amazonian plant Duguetia sthelechantha, and has been proven to be a pigment producer. Considering the high productivity of this species and the lack of data on its chemical composition, the present study aimed to characterize the chemical profile of P. meliponae and evaluate the influence of agitation and the use of different culture media
2023-02-14 | MSV000091281 | MassIVE
Project description:Endophytic bacteria influence plant growth and development and therefore are an attractive resource for applications in agriculture. However, little is known about the impact of these microorganisms on secondary metabolite (SM) production by medicinal plants. Here we assessed, for the first time, the effects of root endophytic bacteria on the modulation of SMs in the medicinal plant Lithospermum officinale (Boraginaceae family), with a focus on the naphthoquinones alkannin/shikonin (A/S). The study was conducted using a newly developed in vitro system as well as in the greenhouse. Targeted and non-targeted metabolomics approaches were used and supported by expression analysis of the gene PGT, encoding a key enzyme in the A/S biosynthesis pathway. Three bacterial strains, Chitinophaga sp. R-73072, Xanthomonas sp. R-73098 and Pseudomonas sp. R-71838 induced a significant increase of diverse SMs, including A/S, in L. officinale in both systems, demonstrating the strength of our approach for screening A/S derivative-inducing bacteria. Our results highlight the impact of root-endophytic bacteria on secondary metabolism in plants and indicate that production of A/S derivatives in planta likely involves cross-modulation of different metabolic pathways that can be manipulated by bacterial endophytes.
2021-08-11 | ST002062 | MetabolomicsWorkbench