Oryza sativa Japonica Group cultivar:Nipponbare
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ABSTRACT:
PROVIDER: PRJNA489273 | ENA |
REPOSITORIES: ENA
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Project description:Herbaspirillum seropedicae is a Betaproteobacterium capable of colonizing epiphytically and endophytically commercial grasses, promoting plant growth. In this study, we utilized RNA-seq to compare the transcriptional profiles of planktonic and maize root-attached H. seropedicae SmR1.
2015-02-28 | E-MTAB-3026 | biostudies-arrayexpress
Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.
2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
Project description:Herbaspirillum seropedicae is an endophytic bacterium that can fix nitrogen and promote a hormonal imbalance that leads to a plant growth-promoting effect when used as a microbial inoculant. Studies focused on mechanisms of action are crucial for a better understanding of the bacteria-plant interaction and optimization of plant growth-promoting response. The work aims to understand the underlined mechanisms responsible for the early stimulatory growth effects of the H. seropedicae inoculation in maize. To perform it, we combined transcriptomic and proteomic approaches with physiological analysis. The results obtained with the inoculation showed increased root biomass (233 and 253%) and shoot biomass (249 and 264%), respectively, for the fresh and dry mass of maize seedlings and increased green content and development. Omics data analysis for the positive biostimulation phenotype revealed that inoculation increases N-uptake and N-assimilation machinery through differential expressed nitrate transporters and amino acids pathway, as well carbon/nitrogen metabolism integration by the tricarboxylic acid cycle and the polyamines pathway. Additionally, phytohormone levels of root and shoot tissues increased in bacterium-inoculated-maize plants leading to feedback regulation by the ubiquitin-proteasome system. The early biostimulatory effect of H. seropedicae partially results from hormonal imbalance coupled with efficient nutrient uptake-assimilation and a boost in primary anabolic metabolism of carbon-nitrogen integrative pathways.
2023-03-11 | PXD038609 | Pride
Project description:Several reports have described the involvement of miRNAs in abiotic stresses. However, their role in biotic stress or to beneficial microbes has not been fully explored. In order to understand on the epigenetic regulation in plant in response to nitrogen-fixing bacteria association, we analyzed the sRNA regulation in maize hybrids (Zea mays M-bM-^@M-^S UENF 506-8) inoculated with the beneficial diazotrophic bacteria (Herbaspirillum seropedicae). Deep sequencing analysis was carried out to identify the sRNAs regulated in maize during association with diazotrophic bacteria. For this analysis, maize plants were germinated in wet paper and put in hydroponic system with HoaglandM-bM-^@M-^Ys solution and then inoculated with H. seropedicae for seven days. Mock and inoculated plants were collected and total RNA from a pool of samples was extracted with Trizol reagent. The two sRNA libraries were sequenced by Illumina. The sequences were filtered to remove adaptors and contaminants rRNA and tRNAs, and sequences with 18-28 nt in length were selected. To identify the miRNAs present in these libraries, we used two strategies using the same website (http://srna-tools.cmp.uea.ac.uk): one to identify novel miRNAs using the maize genome (verson 2) and miRCat pipeline; and other to identify conserved miRNAs using the miRBase database (release 13.0, http://microrna.sanger.ac.uk) and miRProf pipeline. We identified 17 novel putative miRNAs candidates and mapped the precursor of these miRNAs in the maize genome. Furthermore, we identified 25 conserved miRNAs families and the differential expressions were analyzed with miRProf pipeline. The bioinformatics analysis of four up-regulated miRNAs (miR397, miR398, miR408 and miR528) in inoculated plant was validated using stemM-bM-^@M-^Sloop RT-PCR assay. Our findings contribute to increase the knowledge of the molecular relation between plants and endophytic bacteria. Screenning of sRNA transcriptome of maize plants inoculated with Herbaspirillum seropedicae after seven days
2013-08-01 | E-GEOD-47886 | biostudies-arrayexpress
Project description:Transcriptome analysis of leaf or root samples in chitin-treated rice
| PRJDB11867 | ENA
Project description:Herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. Flavonoids such as naringenin, have been shown to have an effect on the interaction between H. seropedicae and its host plants. We used a high-throughput sequencing based method (RNA-Seq) to access the influence of naringenin on the whole transcriptome profile of H. seropedicae.
2015-04-30 | E-MTAB-3435 | biostudies-arrayexpress
Project description:RNA-Seq reads of rice root under 2mM and 0.1mM nitrogen (NH4+) conditions
| PRJDB12563 | ENA
Project description:Herbaspirillum seropedicae SmR1 was grown in NFbHPN medium until OD600nm of 0.6, when 5mM phenol or 2,5mM benzoic acid was added to the medium. After 30 minutes of growth, the cells were collected by centrifugation and total RNA was extracted with RiboPureBacteria. Also, a derivative strain from Herbaspirillum seropedicae SmR1 resistant to 1mM phenol (named strain RP) was grown in NFbHPN medium containing 1mM phenol until OD600nm of 0.6, then 5mM phenol was added to the medium. After 30 minutes of growth, the cells were collected by centrifugation and total RNA was extracted with RiboPureBacteria. All samples were depleted for ribossomal RNA e sequenced with Solid plataform.
2016-04-01 | E-MTAB-3467 | biostudies-arrayexpress
Project description:Transcript analysis of nitrogen response in rice
| PRJNA260890 | ENA
Project description:It was investigated the changes in protein expression in maize roots in response to treatment with Herbaspirillum seropedicae. To identify maize proteins whose expression levels were altered in the presence of bacteria, a label-free quantitative proteomic approach was used.
2024-07-02 | PXD019200 | Pride