GEO DataSets

(Submitter supplied) A time-course transcriptomic study was performed on mature nodules of Lotus japonicus MG-20 at 4 weeks post-inoculation (wpi) with Mesorhizobium loti MAFF303099. Plants were exposed to 10 mM KNO3 for six days and then nitrate was removed for five more days.

Organism:

Lotus japonicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30948

36 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Lotus japonicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30948

6 Samples

Download data: TXT

(Submitter supplied) To identify binding sites and nodule SAGs that are directly targeted by NAC094, we used DAP-seq, which allows the capture of the NAC094 regulatory targets at the whole-genome scale. A total of 2,819 binding peaks corresponding to 2,721 genes were identified from two repeats of the DAP-seq experiment.

Organism:

Lotus japonicus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30948

3 Samples

Download data: BW

(Submitter supplied) Key genes involved in symbiosis have been lost in nonmycorrhizal plants such as Arabidopsis thaliana. We studied the effects on gene expression in A. thaliana expressing an abbreviated, functional version of one of genes, the transcription factor Interacting Protein of DMI3 (IPD3-min), under low nutrient conditions in the presence and absence of a mycorrhizal fungi, Rhizophagus. We conducted the same transcriptome analysis with a cyclops-4 knockout mutant in Lotus japonicus to compare with the expression profile of a mycorrhizal host model lacking IPD3.

Organism:

Arabidopsis thaliana; Lotus japonicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33123 GPL28290

44 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Lotus japonicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32775

36 Samples

Download data: RDS

(Submitter supplied) In this study, we have manually separated two main types of cells in mature nodules, known as infected cells (ICs) and uninfected cells (UCs). Smart-Seq2 mediated single-cell RNA sequencing reveals that 939 genes are significantly differentially expressed between ICs and UCs, including transcription factors, transporters, and catalytic enzymes. our data provide valuable resources for investigating genetic components responsible for the differentiated but coordinated cellular process between ICs and UCs. more...

Organism:

Lotus japonicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30948

8 Samples

Download data: TXT

(Submitter supplied) Since roots showed different developmental responses to the two compounds, we asked whether this was also reflected in the transcriptome

Organism:

Lotus japonicus

Type:

Expression profiling by array

Platform:

GPL29300

27 Samples

Download data: CEL

(Submitter supplied) RNA-seq analysis was performed to know the expression profiles of Lotus japonicus genes during nodule development and nitrogen fixation.

Organism:

Lotus japonicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26502

14 Samples

Download data: TXT

(Submitter supplied) Drought is one of the major environmental factors limiting biomass and seed yield production in agriculture. In this research we focused on plants from Fabaceae family, which have a unique ability for establishment of symbiosis with nitrogen-fixing bacteria, and are relatively susceptible to water limitation. We present the changes in nitrogenase activity and global gene expression occurring in Medicago truncatula and Lotus japonicus root nodules during water deficit. more...

Organism:

Sinorhizobium meliloti; Mesorhizobium loti; Lotus japonicus; Medicago truncatula

Type:

Expression profiling by high throughput sequencing

4 related Platforms

16 Samples

Download data: XLSX

(Submitter supplied) Natural DNA methylation variation was examined in a population of wild Lotus japonicus accessions from Japan

Organism:

Lotus japonicus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20925

20 Samples

Download data: TXT

(Submitter supplied) Whole genome DNA methylation data for the the Lotus japonicus accession 'Gifu'

Organism:

Lotus japonicus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20925

1 Sample

Download data: TXT

(Submitter supplied) DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. more...

Organism:

Populus trichocarpa; Erythranthe guttata; Eutrema salsugineum; Beta vulgaris; Panicum hallii; Medicago truncatula; Setaria viridis; Sorghum bicolor; Vitis vinifera; Theobroma cacao; Brassica rapa; Malus domestica; Ricinus communis; Brachypodium distachyon; Lotus japonicus; Citrus x clementina; Cannabis sativa; Cucumis sativus; Prunus persica; Manihot esculenta; Panicum virgatum; Fragaria vesca; Eucalyptus grandis

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

30 related Platforms

34 Samples

Download data: TSV

(Submitter supplied) Legumes interact with rhizobial bacteria to form nitrogen-fixing root nodules. Host signalling following mutual recognition ensures a specific response, but is only partially understood. Focusing on the stage of epidermal infection with Mesorhizobium loti, we analysed endogenous small RNAs (sRNAs) of the model legume Lotus japonicus to investigate their involvement in host response regulation. We used Illumina sequencing to annotate the L. more...

Organism:

Lotus japonicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL20925 GPL21565

4 Samples

Download data: XLSX

(Submitter supplied) Canola (oilseed rape, Brassica napus L.), is susceptible to infection by the biotrophic protist Plasmodiophora brassicae, the causal agent of clubroot. To understand the roles of microRNAs (miRNAs) during the post-transcriptional regulation of disease initiation and progression, we have characterized the changes in miRNA expression profiles in canola roots during clubroot disease development and have compared these to uninfected roots. more...

Organism:

Pinus taeda; Liriodendron tulipifera; Phaseolus vulgaris; Ipomoea batatas; Lactuca sativa; Oryza rufipogon; Oryza nivara; Sorghum bicolor; Rorippa indica; Prunus salicina; Populus tremula; Malcolmia maritima; Picea sitchensis; Brassica napus; Lupinus luteus; Phaseolus coccineus; Manihot esculenta; Ricinus communis; Oryza brachyantha; Cenchrus americanus; Phleum pratense; Panicum virgatum; Nuphar advena; Physcomitrium patens; Persea americana; Populus trichocarpa x Populus deltoides; Malus domestica; Nicotiana sylvestris; Nicotiana tabacum; Petunia x hybrida; Oryza sativa; Lolium arundinaceum; Lotus japonicus; Cenchrus ciliaris; Populus tremula x Populus tremuloides; Nasturtium officinale; Picea glauca; Populus tremuloides; Populus trichocarpa; Prunus persica; Medicago truncatula; Nicotiana benthamiana; Hordeum vulgare; Ipomoea nil; Prunus armeniaca; Peridictyon sanctum; Oryza barthii; Hordeum vulgare subsp. vulgare; Oenocarpus bataua

Type:

Non-coding RNA profiling by array

Platform:

GPL17805

4 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Lotus japonicus

Type:

Expression profiling by array

Platform:

GPL14826

9 Samples

Download data: TXT

(Submitter supplied) To identify the regulatory targets of the R2R3-Myb transcription factor, LjMyb14, the gene was constitutively over-expressed in Lotus japonicus under the Lotus ubiquitin promoter.

Organism:

Lotus japonicus

Type:

Expression profiling by array

Platform:

GPL14354

6 Samples

Download data: TXT

(Submitter supplied) To identify transcription factors involved in the production of defense-related phytochemicals through co-expression studies.

Organism:

Lotus japonicus

Type:

Expression profiling by array

Platform:

GPL14118

10 Samples

Download data: TXT