Bacteria
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ABSTRACT:
PROVIDER: PRJNA1066520 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Symbiotic legume nodules and lateral roots arise away from the root meristem via dedifferentiation events. While these organs share some morphological and developmental similarities, whether legume nodules are modified lateral roots is an open question. We dissected emerging nodules (EN), mature nodules (MN), emerging lateral roots (ELR) and young lateral roots (YLR), and constructed strand-specific RNAseq libraries using polyA-enriched RNA preparations. Root sections above and below these organs devoid of any lateral organs were used to construct respective control tissue libraries (ABEN, ABMN, ABELR, ABYLR respectively). High sequence quality, predominant mapping to coding sequences, and consistency between replicates indicated that the RNAseq libraries were of very high quality. We identified genes enriched in emerging nodules, mature nodules, emerging lateral roots and young lateral roots in soybean by comparing global gene expression profiles between each of these organs and adjacent root segments. Potential uses for this high quality transcriptome data set include generation of global gene regulatory networks to identify key regulators; metabolic pathway analyses and comparative analysis of key gene families to discover organ-specific biological processes; and identification of organ-specific alternate spliced transcripts. When combined with other similar datasets especially from leguminous plants these analyses can help answer questions on the evolutionary origins of root nodules and relationships between the development of different plant lateral organs.
2019-04-10 | GSE129509 | GEO
Project description:WUYAO-Lindera aggregata (Sims) Kosterm.
For analysis the raw and processed Lindera aggregata (Sims) Kosterm.
2022.10.17
2023-02-06 | MSV000091210 | MassIVE
Project description:The microRNA390 targets the TAS3 transcript leading to the production of trans-acting small interference RNAs that subsequently post-transcriptionally repress the mRNAs encoding the Auxin Response Factors (ARF)2, ARF3, and ARF4. This module has been linked to the development of lateral organs in both aerial and underground tissues. Previously, we have shown that the miR390/TAS3/ARFs module mediates the control of lateral roots and symbiotic nodules in legumes. Here, we show that a member of the Lateral Organ Boundaries Domain (LBD) family of transcription factors, designated as MtLBD17/29a, is a target of the miR390/TAS3/ARFs module. Transcriptomic, RT-qPCR and promoter fusion analysis revealed that MtLBD17/29a is induced under symbiotic conditions, whereas no induction was observed in roots overexpressing miR390 or silenced in ARF2/3/4. ChIP-PCR experiments demonstrated that MtARF2 directly binds to an Auxin Response Element (ARE) present in the MtLBD17/29a promoter activating its expression. Knockdown of MtLBD17/29a reduced the length of primary and lateral roots and increasing the density of lateral roots, whereas overexpression of MtLBD17/29a produced the opposite phenotype. Interestingly, both knockdown and overexpression of MtLBD17/29a resulted in a significant reduction in the number of nodules and infection events, as well as impaired the induction of the symbiotic genes Nodulation Signaling Pathway (NSP) 1 and 2, reminiscent of the phenotype observed in ARF2/3/4 silenced roots. These results demonstrate that MtLBD17/29 is regulated by the miR390/TAS3/ARFs module and a direct target of ARF2, revealing a new lateral root regulatory hub recruited by legumes to act in the root nodule symbiotic program.
2024-04-15 | GSE248872 | GEO
Project description:The association between soil microbes and plant roots is present in all natural and agricultural environments. Microbes can be beneficial, pathogenic, or neutral to the host plant development and adaptation to abiotic or biotic stresses. Progress in investigating the functions and changes in microbial communities in diverse environments have been rapidly developing in recent years, but the changes in root function is still largely understudied. The aim of this study was to determine how soil bacteria influence maize root transcription and microRNAs (miRNAs) populations in a controlled inoculation of known microbes over a defined time course. At each time point after inoculation of the maize inbred line B73 with ten bacterial isolates, DNA and RNA were isolated from roots. The V4 region of the 16S rRNA gene was amplified from the DNA and sequenced with the Illumina MiSeq platform. Amplicon sequencing of the 16S rRNA gene indicated that most of the microbes successfully colonized maize roots. The colonization was dynamic over time and varied with the specific bacterial isolate. Small RNA sequencing and mRNA-Seq was done to capture changes in the root transcriptome from 0.5 to 480 hours after inoculation. The transcriptome and small RNA analyses revealed epigenetic and transcriptional changes in roots due to the microbial inoculation. This research provides the foundational data needed to understand how plant roots interact with bacterial partners and will be used to develop predictive models for root response to bacteria.
2023-05-01 | GSE214656 | GEO
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:Root-microbe interaction and its specialized root nodule structures and functions are well studied. In contrast, leaf nodules harboring microbial endophytes in special glandular leaf structures have only recently gained increased interest as plant-microbe phyllosphere interactions. Here, we applied a comprehensive metabolomics platform in combination with natural product isolation and characterization to dissect leaf and leaf nodule metabolism and functions in <i>Ardisia crenata</i> (Primulaceae) and <i>Psychotria punctata</i> (Rubiaceae). The results indicate that abiotic stress resilience plays an important part within the leaf nodule symbiosis of both species. Both species showed metabolic signatures of enhanced nitrogen assimilation/dissimilation pattern and increased polyamine levels in nodules compared to leaf lamina tissue potentially involved in senescence processes and photosynthesis. Multiple links to cytokinin and REDOX-active pathways were found. Our results further demonstrate that secondary metabolite production by endophytes is a key feature of this symbiotic system. Multiple anhydromuropeptides (AhMP) and their derivatives were identified as highly characteristic biomarkers for nodulation within both species. A novel epicatechin derivative was structurally elucidated with NMR and shown to be enriched within the leaf nodules of <i>A. crenata</i>. This enrichment within nodulated tissues was also observed for catechin and other flavonoids indicating that flavonoid metabolism may play an important role for leaf nodule symbiosis of <i>A. crenata.</i> In contrast, pavettamine was only detected in <i>P. punctata</i> and showed no nodule specific enrichment but a developmental effect. Further natural products were detected, including three putative unknown depsipeptide structures in <i>A. crenata</i> leaf nodules. The analysis presents a first metabolomics reference data set for the intimate interaction of microbes and plants in leaf nodules, reveals novel metabolic processes of plant-microbe interaction as well as the potential of natural product discovery in these systems.
2021-08-26 | MTBLS2870 | MetaboLights
Project description:Legumes interact with soil microbes, leading to the development of nitrogen-fixing root nodules and arbuscular mycorrhizal (AM) roots. While nodule initiation by diffusible lipochitooligosaccharide (LCO) Nod-factors of bacterial origin (Nod-LCOs) is well characterized, diffusible AM fungal signals were only recently identified as sulphated and non-sulphated LCOs (sMyc-LCOs and nsMyc-LCOs). Applying Myc-LCOs in parallel to Nod-LCOs, we used GeneChips to detail the global programme of gene expression in response to the external application of symbiotic LCOs.
2012-05-31 | GSE33636 | GEO
Project description:12plex_medicago_2012-03 - mtefd1 and wt roots and nodules - Identification of genes affected by a KO mutation in a transcription factor involved in root and nodule development, MtEFD1. - Comparison of wild type and efd-1 transcriptomes in non inoculated nitrogen-starved control roots and nodules at 4 dpi, 6 and 11 dpi. Comparison of wild type nodule (11 dpi) and root transcriptomes, using mixed random primed and polydT primed probes.
2019-10-16 | GSE138899 | GEO