Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq Transcriptional Profiling of Herbaspirillum seropedicae Colonizing Bread Wheat (Triticum aestivum) Roots.

ABSTRACT: H. seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize and promote plant growth wheat seedlings growing hydroponically in Hoaglandâs medium were inoculated with H. seropedicae the bacteria and incubated for 3 days. mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of bacteria attached to the root and planktonic revealed an extensive metabolic adaptation to the epiphytic life style.

INSTRUMENT(S): AB SOLiD 3 Plus System

ORGANISM(S): Herbaspirillum seropedicae SmR1

SUBMITTER: VĂ˘nia Pankievicz

PROVIDER: E-MTAB-3646 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

Dataset Information

RNA-seq Transcriptional Profiling of Herbaspirillum seropedicae Colonizing Bread Wheat (Triticum aestivum) Roots.

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