Root nodule microbiome of Lotus tenuis
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ABSTRACT:
PROVIDER: PRJNA990473 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNA-seq analysis was performed to know the expression profiles of Lotus japonicus genes during nodule development and nitrogen fixation.
2019-12-31 | GSE129778 | GEO
Project description:Legume plants can establish symbiotic nitrogen fixation (SNF) with rhizobia mostly in root nodules, where rhizobia-infected cells are accompanied with uninfected cells in a mosaic pattern. Inside the mature nodules of legume, carbon and nitrogen nutrients between host plant cells and their resident bacteria are actively exchanged. To elucidate the metabolite dynamics relevant for SNF in nodules, three cell-types from nodule tissues of a model legume, Lotus japonicus, were isolated using laser microdissesction, and transcriptome analysis was done by an oligoarray with 60-mer length representing 21,495 genes. In our cell-type-specific profiling, many genes were identified as being expressed in nodules with spatial-specific manners. Among them, genes coding for metabolic enzymes were classified according to their function, and detailed data analysis figured out that secondary metabolic pathway was highly activated in nodule cortex. In particular, a number of metabolic genes for phenyl propanoid pathway were found as highly expressed genes accompanied with those encoding putative transporters of secondary metabolites. These data suggest the involvement of novel physiological function of phenylpropanoids in SNF. Gene expression in three different cell-types of Lotus japonicus nodule was measured. Three independent experiments were performed at each cell-types.
2011-12-29 | E-GEOD-34753 | biostudies-arrayexpress
Project description:To investigate the function of NAC094 in vivo, we overexpressed NAC094 in the infected cells of nodules using an L. japonicus Lb2 expression cassette. To this end, we used a GUS overexpression construct as control and analysed stably transformed plants to detect symbiotic phenotypes. Results show that overexpression of NAC094 causes premature senescence of nodules. To identify the mechanism by which NAC094 regulates nodule senescence, we performed a transcriptome profiling analysis of nodules at 3 wpi. Around 13,850 differentially expressed genes (DEGs) were identified by comparing NAC-OE with control nodules (Log2FC > 1, FDR < 0.05). Of these, 7,516 were up-regulated (NAC-OE-UP) and 6,334 were down-regulated (NAC-OE-DOWN).
2023-03-23 | GSE197361 | GEO
Project description:Legume plants can establish symbiotic nitrogen fixation (SNF) with rhizobia mostly in root nodules, where rhizobia-infected cells are accompanied with uninfected cells in a mosaic pattern. Inside the mature nodules of legume, carbon and nitrogen nutrients between host plant cells and their resident bacteria are actively exchanged. To elucidate the metabolite dynamics relevant for SNF in nodules, three cell-types from nodule tissues of a model legume, Lotus japonicus, were isolated using laser microdissesction, and transcriptome analysis was done by an oligoarray with 60-mer length representing 21,495 genes. In our cell-type-specific profiling, many genes were identified as being expressed in nodules with spatial-specific manners. Among them, genes coding for metabolic enzymes were classified according to their function, and detailed data analysis figured out that secondary metabolic pathway was highly activated in nodule cortex. In particular, a number of metabolic genes for phenyl propanoid pathway were found as highly expressed genes accompanied with those encoding putative transporters of secondary metabolites. These data suggest the involvement of novel physiological function of phenylpropanoids in SNF.
2011-12-29 | GSE34753 | GEO
Project description:Legumes establish endosymbiotic associations with nitrogen-fixing rhizobia, which they host inside root nodules. Here, specific physiological and morphological adaptations, such as the production of oxygen-binding leghemoglobin proteins and the formation of an oxygen diffusion barrier in the nodule periphery, are essential to protect the oxygen-labile bacterial nitrogenase enzyme. The molecular basis of the latter process remains elusive, as the identification of required genes is limited by the epistatic effect of nodule organogenesis over nodule infection and rhizobia accommodation. We overcame this by exploring the phenotypic diversity of Lotus japonicus accessions that uncouple nodule organogenesis from nodule infection when inoculated with a sub-compatible Rhizobium strain. Using comparative transcriptomics, we identified genes with functions associated with oxygen homeostasis and deposition of lipid polyesters on cell walls to be specifically upregulated in infected compared to uninfected nodules. As such hydrophobic modifications on cell walls are pivotal for creating diffusion barriers like the root endodermis, we focused on two Fatty acyl-CoA reductase genes that were specifically activated in the nodule or in the root endodermis. Mutant lines in a Fatty acyl-CoA reductase gene expressed exclusively in the nodule endodermis showed had decreased suberization of this cell layer and increased nodule permeability compared to wild type plants. Oxygen concentrations were significantly increased in the inner cortex of mutant nodules, which correlated with reduced nitrogen fixation rates, and impaired shoot growth. These results provide the first genetic evidence for the formation of the nodule oxygen diffusion barrier, a key adaptation enabling nitrogen fixation in legume nodules.
2022-11-01 | GSE216502 | GEO
Project description:Lotus japonicus is a perennial legume with a small diploid genome that has been adopted as a model species for legume genetics and genomics. With the genome sequence as a backdrop (Sato et al. 2008), we have generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, including nodule and seed development.
2010-12-22 | E-MEXP-1726 | biostudies-arrayexpress
Project description:12plex_medicago_2014_02 - nar nodule vs root transcriptome - which are the genes differentially expressed in alfalfa spontaneous (non rhizobium-infected) nodules vs. control roots? - biological material: aeroponically grown cuttings of a Medicago sativa (alfalfa) accession that produces empty nodules when nitrogen-starved. Samples for transcriptome comparison: isolated NAR nodules (10 days post N-starvation) vs. roots of the same plants (pools of 3 roots).
2018-11-01 | GSE121571 | GEO
Project description:To understand the role of Medicago truncatula NODULE INCEPTION (MtNIN) in nodule development, we analyzed the transcriptome of roots ectopically overexpressing NIN, nodules of weak mutant allele nin-16, and nodules of dnf1-2 mutant.
2021-11-09 | GSE178119 | GEO
Project description:We have undertaken a detailed study to identify mechanisms regulating expression of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in different stages of nodule development. Additionally, rhizobial mutants were used to understand the importance of the rhizobial components in induction of NCRs. Early NCRs were detected during the initial infection of rhizobia in nodules and continue to be expressed into the late stages of nodule development. Late NCRs were induced concomittant with bacteroid development in the nodules. The induction of these groups of genes was correlated with the number and morphology of rhizobia in the nodule.
2013-03-05 | GSE34803 | GEO