Miscanthus transmorrisonensis strain:EF0143 | cultivar:Evergreen Maiden Grass EF0143
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ABSTRACT:
PROVIDER: PRJNA337566 | ENA |
REPOSITORIES: ENA
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Project description:The aims of our study were: 1) to elucidate physiological responses in three Miscanthus species and newly bred triploid hybrid in three water stress treatment conditions 2) utilise the induced physiological conditions for an in-depth transcriptome study on the molecular basis of water stress in Miscanthus spp.
2020-09-30 | E-MTAB-9354 | 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 different Miscanthus x giganteus tissues (including leaves, flowers, and rhizomes). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features such 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 genome under study.
2010-01-27 | GSE20056 | GEO
Project description:Miscanthus sacchariflorus cultivar:Silver Banner Grass EF03(58-60) Genome sequencing
| PRJNA337641 | ENA
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 different Miscanthus x giganteus tissues (including leaves, flowers, and rhizomes). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features such 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 genome under study. Small RNA libraries were derived from leaves, flowers and rhizomes of Miscanthus x giganteus. Each tissue represented a mixture of developmental stages, with a bias towards those from early, actively differentiating cells. For rhizomes, the apical tip portion was collected. 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 Steven Moose for providing the plant material and Kan Nobuta for assistance with the computational methods.
2010-01-27 | E-GEOD-20056 | biostudies-arrayexpress
Project description:Grass pea seeds and seedlings protein extracts were chromatographically fractionated. To identify the β-ODAP synthase enzyme, active fractions, as determined by a colorimetric assay that detects the presence of a derivative of free L-α,β-diaminopropionic acid (L-DAPA), were subjected to tryptic digestion and LC-MS/MS and searched against a database containing translated sequences from a long-read PacBio mRNA sequencing of grass pea seeds and seedlings.
2022-05-19 | PXD030847 | Pride
Project description:Adult male grass shrimp were exposed for 96 hours to LC50 concentrations of either Fipronil, Endosulfan, or Cadmium, as well as a Carrier Control exposure. RNA was extracted from whole-body homogenates using the RNABee kit. Tags were clustered to identify tags diagnostic of the different exposures. Keywords: SAGE, Grass shrimp, ecotoxicogenomics
2006-05-18 | GSE4853 | GEO
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in grass-clump dwarf lines, which are synthetic hexaploid lines from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon or T. turgidum ssp. carthlicum) and diploid wheat progenitor Aegilops tauschii (KU2025). No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Together with small RNA sequencing analysis of the grass-clump dwarf line, unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype.
2016-03-02 | GSE78784 | GEO
Project description:Purpose:Salinity is an important environmental factor that affects the physiological activities of fish. The goals of this study are investigating the effect of different saline-alkali stress on grass carp (Ctenopharyngodon idella). Methods: Grass carp individuals, averaging 12 cm in body length, were obtained from Duofu fish farm (Wuhan, China) and cultured at recirculating aquaculture system for 2 weeks before the experiment began. For the challenge, all grass carp were randomly divided into three groups, and then cultured at saline-alkali water with the concentration of 0, 3‰ and 6‰. After 30 days, some grass crap cultured at 3‰ and 6‰ saline-alkali water were injured. At the same time, gill samples of grass carp were collected from 0, 3‰ (grass carp was not injured), 3‰ (grass carp was injured), 6‰ (grass carp was not injured) and 6‰ (grass carp was injured)saline-alkali groups. Total RNA of all samples was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's introduction. RNA integrity was assessed using an Agilent 2100 bioanalyzer (Agilent, USA). Samples with RNA integrity numbers (RINs) ≥ 7.5 were subjected to cDNA library construction using TruseqTM RNA sample prep Kit (Illumina). Results:A total of 15 were processed for transcriptome sequencing, generating 94.99Gb Clean Data. At least 5.76Gb clean data were generated for each sample with minimum 91.87% of clean data achieved quality score of Q30. Clean reads of each sample were mapped to specified reference genome. Mapping ratio ranged from 88.59% to 92.84%. The expression of genes was quantified and differentially expressed genes were identified based on their expression.Criteria for differentially expressed genes was set as Fold Change(FC)≥1.5 and Pvalue<0.05. Fold change(FC) refers to the ratio of gene expression in two samples. These DEGs were further processed for functional annotation and enrichment analysis. Conclusions: Our study represents Effects and molecular regulation mechanisms of saline-alkali stress on the healthy grass carp by using RNA-seqtechnology. Our results show that saline-alkali stress will impair the immune system of grass carp.
2021-12-31 | GSE185170 | GEO
Project description:Resistance to herbicides in weeds can be due to alteration(s) in the gene encoding the herbicide target site, or to herbicide degradation via a deviation in plant general metabolism. If target-site-based resistance is easy to study, the multigenic control of metabolism-based resistance renders it much more complex to study. Metabolism-based resistance to herbicides represents the major part of herbicide resistance in black-grass. Its most likely basis is an overexpression of genes encoding enzymes degrading herbicides. We thus seek to identify such overexpressed genes by comparing the transcriptomes of resistant and sensitive black-grass individuals belonging to an F2 line segregating for two resistance genes. Given there are no genomic tools developed for black-grass, this approach will use heterologous hybridisation onto a wheat Affymetrix microarray. Comparison using heterologous hybridisation onto a wheat whole-genome microarray of transcriptome of three pools of black-grass plants obtained 2h30 after herbicide spraying at field rate. The three pools correspond to: · Sensitive plants (killed by herbicide). · Moderately resistant plants (growth impaired by herbicide but plants still alive) · Resistant plants (growth unimpaired by herbicide)
2010-05-04 | GSE15864 | GEO
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in grass-clump dwarf lines, which are synthetic hexaploid lines from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon or T. turgidum ssp. carthlicum) and diploid wheat progenitor Aegilops tauschii (KU2025). No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Together with small RNA sequencing analysis of the grass-clump dwarf line, unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype. Expression patterns were compared between the three synthetic hexaploid lines showing the wild-type phenotype (as a reference) and grass-clump dwarf. Total RNA samples were isolated from crown tissues of the plants grown at 24°C under long day (18-h light and 6-h dark) condition for 8 weeks. Two independent experiments were conducted in each exprement.
2016-03-02 | E-GEOD-78784 | biostudies-arrayexpress