Rhizosphere metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA725990 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14629452_1.fastq.gz | Fastqsanger.gz | |||
| SRR14629452_2.fastq.gz | Fastqsanger.gz | |||
| SRR14629453_1.fastq.gz | Fastqsanger.gz | |||
| SRR14629453_2.fastq.gz | Fastqsanger.gz | |||
| SRR14629454_1.fastq.gz | Fastqsanger.gz |
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Project description:The rhizosphere microbiome plays an essential role in enhancing the growth of plants, raising the need for comprehension of their metabolic abilities. Here, we investigated rhizospheric and bulk soils of maize plants in Mafikeng, South Africa. Metagenome-assembled genomes containing plant growth-promoting genes were reconstructed.
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Project description:modENCODE_submission_2621 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP177(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The EGL-27::EGFP fusion protein is expressed in the correct egl-27 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-27 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119) official name : OP177 ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene egl-27; Strain OP177(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The EGL-27::EGFP fusion protein is expressed in the correct egl-27 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-27 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119) official name : OP177 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq
2011-02-18 | E-GEOD-25809 | biostudies-arrayexpress
Project description:modENCODE_submission_3159 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP54 (official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene egl-5; Strain OP54 (official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim ); temp (temperature) 20 degree celsius
2011-03-31 | E-GEOD-25796 | biostudies-arrayexpress
Project description:Wheat is the major crop in India and like other crops also subjected to influence by microbial communities of the rhizospheric region which are extremely diverse and undoubtedly play a central role in the nutrient cycle, plant productivity and growth promotion. In order to know how changes in the rhizospheric microbial community can make an impact on overall crop function, wheat rhizospheric soil samples from Ghazipur (25.913824 N 83.529715 E) regions of Eastern Uttar Pradesh (Eastern Indogangatic Plain), were collected and analyzed. Full length 16S rRNA gene amplification sequencing was performed to reveal the bacterial community in wheat rhizosphere. A total of 51,909 read were analyzed, out of that only 44,125 reads were classified and 7784 were unclassified using oxford nanopore sequencing and EPI2ME data analysis platform. MinION oxford nanopore sequencing uncovered that dominant phyla were Proteobacteria (68%), followed by firmicutes (13%), bacteroidetes (3%), actinobacteria (3%) and acidobacteria (3%). The data is available at the NCBI - Sequence Read Archive (SRA) with accession number: SRX5275271.
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Project description:Mineral phosphate solubilization (MPS) microorganisms are important for their provision of orthophosphate anions for plant growth promotion activity in soil. In this study, we applied a functional metagenomic approach to identify this trait directly from the microbiome in barley rhizosphere soil that had not received P fertilizer over a 15-year period. A fosmid system was used to clone the metagenome of which 18,000 clones (~666 Mb of DNA) was screened for MPS. Functional assays and High Performance Liquid Chromatography analysis recognized gluconic acid production and MPS activity in the range 24.8-77.1 mmol/L and 27.6-38.16 μg/mL, respectively, when screened in an Escherichia coli host (at frequency of one MPS-positive clone hit per 114 Mb DNA tested). The MPS clones (with average insert size of ~37 kb) were analysed by 454 Roche sequencing and annotated. A number of genes/operons with homology to Phosphorous (P) uptake, regulatory and solubilization mechanisms were identified, linking the MPS function to the uncultivated microbiome present in barley rhizosphere soil.
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2020-09-15 | GSE157928 | GEO
Project description:Metal resistance determinants have traditionally been found in cultivated bacteria. To search for genes involved in nickel resistance, we analyzed the bacterial community of the rhizosphere of Erica andevalensis, an endemic heather which grows at the banks of the Tinto River, a naturally metal-enriched and extremely acidic environment in southwestern Spain. 16S rRNA gene sequence analysis of rhizosphere DNA revealed the presence of members of five phylogenetic groups of Bacteria and the two main groups of Archaea mostly associated with sites impacted by acid mine drainage (AMD). The diversity observed and the presence of heavy metals in the rhizosphere led us to construct and screen five different metagenomic libraries hosted in Escherichia coli for searching novel nickel resistance determinants. A total of 13 positive clones were detected and analyzed. Insights about their possible mechanisms of resistance were obtained from cellular nickel content and sequence similarities. Two clones encoded putative ABC transporter components, and a novel mechanism of metal efflux is suggested. In addition, a nickel hyperaccumulation mechanism is proposed for a clone encoding a serine O-acetyltransferase. Five clones encoded proteins similar to well-characterized proteins but not previously reported to be related to nickel resistance, and the remaining six clones encoded hypothetical or conserved hypothetical proteins of uncertain functions. This is the first report documenting nickel resistance genes recovered from the metagenome of an AMD environment.
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