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ABSTRACT: Root nodule microbiome of Lotus tenuis in the Flooding Pampa, Argentina.

PROVIDER: PRJNA1118284 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29267600.fastq.gz	Fastqsanger.gz
	SRR29267553.fastq.gz	Fastqsanger.gz
	SRR29267554.fastq.gz	Fastqsanger.gz
	SRR29267555.fastq.gz	Fastqsanger.gz
	SRR29267556.fastq.gz	Fastqsanger.gz

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Root nodule microbiome of Lotus tenuis

Project description:Root nodule microbiome of Lotus tenuis in the Flooding Pampa, Argentina. Raw sequence reads of plant nodules collected from the field.

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Tissue-specific regulation of lipid polyester synthesis genes controlling oxygen permeation into Lotus japonicus nodules

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.

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Cell-type specific transcriptome analysis in nodules of Lotus japonicus

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

Gene expression during root nodule development in wild type and Fix- mutant of Lotus japonicus

Project description:RNA-seq analysis was performed to know the expression profiles of Lotus japonicus genes during nodule development and nitrogen fixation.

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Project description:Root nodule Microbiome

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Project description:Medicago truncatula engages in root nodule symbiosis by developing a de novo plant organ (known as nodule) in its roots in response to the infection by rhizobia. These nodules are de novo plant organs that provide an optimal environment for the rhizobia to fix nitrogen in exchange for photosynthates. The establishment of root nodule symbioses (RNS) requires the coordination of two distinct processes: bacterial infection and nodule organogenesis. In this study we used single-cell RNA-seq to investigate the first hours of the establishment of the root nodule symbiosis aiming to identify the transcriptional mechanisms governing this process.

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Project description:Acting in a partially redundant manner, NF-Ys were shown previously to regulate bacterial infection, including selection of a superior rhizobial strain, and to participate in mediating nodule structure formation. However, the exact mechanism(s) by which these transcriptional factors exert their symbiotic functions has remained elusive. Gene expression profiling for wild-type and Nuclear Factor YA (nf-ya)-A mutants in roots of Lotus japonicus were conducted 4 days after inoculation with Mesorhizobium loti in order to understand the interaction of NF-Ys and other genes in Lotus japonicus.

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