Root metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA271753 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Illumina HiSeq technology was used to generate mRNA profiles from mycorrhizal Quercus robur roots. Tuber melanosporum, T. aestivum and T.magnatum mycorrhizal root tips were harvested and used for RNA extraction. Paired-end reads of 100 bp were generated and aligned to Quercus robur CDS using CLC Genomics Workbench 9.
2018-07-01 | GSE97122 | GEO
Project description:Root-associated bacterial and fungal communities
| PRJEB32926 | ENA
Project description:Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low-N stress. This indicates that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.
2023-08-29 | MSV000092783 | MassIVE
Project description:Fungal communities associated with Douglas-fir roots
| PRJNA284271 | ENA
Project description:Roots of Arabidopsis thaliana do not engage in symbiotic association with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors having diverse lifestyles and retained diverse repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.
2021-11-03 | GSE169629 | GEO
Project description:Ectomycorrhizal fungal communities associated with eucalyptus in Japan
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Project description:Quercus ilex, Quercus pubescens, Quercus robur Assembly
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Project description:Quercus robur subsp. robur strain:3P Genome sequencing
| PRJNA264613 | ENA