Arabidopsis Root Microbiome
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ABSTRACT:
PROVIDER: PRJNA1141366 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Arabidopsis root bacterial microbiome Metagenome
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Project description:Many Cactaceae species exhibit determinate growth of the primary root as a consequence of root apical meristem (RAM) exhaustion. The genetic regulation of this root growth pattern is unknown. We de novo assembled and annotated the root apex transcriptome of the Pachycereus pringlei primary root at three developmental stages with active or exhausted RAM. The assembled transcriptome was characterized and used to evaluate differential transcript expression, identify RT-qPCR reference genes, and infer a transcriptional regulatory network. We generated a robust and comprehensive transcriptome of the primary root apex of P. pringlei and identified putative orthologs of Arabidopsis regulators of RAM maintenance, as well as putative lineage-specific transcripts. Furthermore, the transcriptome contained putative orthologs of most proteins involved in housekeeping processes, hormone signaling, and metabolic pathways. Specific transcriptional programs operate in the root apex at specific developmental time points. The transcriptional state of the P. pringlei root apex as the RAM becomes exhausted is comparable to that of cells from the meristematic, elongation, and differentiation zones of Arabidopsis roots. We suggest that the genetic program underlying the drought stress response is induced during development of the Cactaceae root, and that lineage-specific transcripts could contribute to root apical meristem exhaustion in Cactaceae.
2018-05-25 | GSE104832 | GEO
Project description:A novel triterpene biosynthetic network mediates Arabidopsis root microbiota assembly
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Project description:Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, it is unclear whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria in the root microbiome. Here we show how flavonoids preferentially attracts Aeromonadaceae in Arabidopsis thaliana root microbiome and how flavonoid-dependent recruitment of an Aeromona spp. results in enhanced plant drought resistance.
2022-10-19 | GSE184872 | GEO
Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
2020-03-06 | GSE146427 | GEO
Project description:The root epidermis of Arabidopsis provides a simple and experimentally useful model for studying the molecular basis of cell fate and differentiation. The goal of this study was to define the larger gene regulatory network that governs the differentiation of the root hair and non-hair cell types of the Arabidopsis root epidermis. Transcript levels in the root epidermis of wild-type and mutant lines were assessed by purifying populations of root epidermal cells using fluorescence-based cell-sorting. Further, the role of the plant hormones auxin and ethylene on root epidermis development was assessed by defining transcript levels in the root epidermis of plants grown on media containing IAA or ACC. These microarray results were used to construct a comprehensive gene regulatory network that depicts the transcriptional control of root epidermal cell fate and differentiation in Arabidopsis.
2011-12-01 | GSE30547 | GEO
Project description:Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity. In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. This series contains the microarray expression data for 7 ecotypes that represent a range of root branching strategies. We used microarrays to detail the global programme of gene expression involved in the plants response to nitrogen in the root and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process.
2013-09-01 | GSE34130 | GEO
Project description:RNASeq of roots from two genotypes of Arabidopsis thaliana plants, Col-0 and myb36-2 grown axenically or with a 41 member bacterial Synthetic Community (SynCom) to explore the interaction between the root diffusion barriers and the root microbiome.
2020-11-01 | GSE151376 | GEO
Project description:Purpose: We aimed to compare transcriptomic changes after melatonin (MT) and IAA treatments in Arabidopsis and dissected cross-talk between MT and IAA Methods: A total amount of 1 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq2000 platform and paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0). Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified coregulated genes by melatonin and IAA in Arabidopsis seedlings
2021-12-21 | GSE152813 | GEO
Project description:Purpose: We aimed to compare transcriptomic changes after melatonin (MT) and IAA treatments in Arabidopsis and dissected cross-talk between MT and IAA Methods: A total amount of 1 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq2000 platform and paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0). Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified coregulated genes by melatonin and IAA in Arabidopsis seedlings
2021-08-11 | GSE167524 | GEO