Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNAseq analyses of pathogenic Burkholderia glumae under in vitro and in vivo conditions

ABSTRACT: We analyzed B. glumae transcriptome from infected rice tissue using an RNAseq technique. To identify unique expression of B. glumae genes within rice tissues, we compared in vivo transcriptome data of B. glumae to in vitro data. To accomplish this, we analyzed differentially expressed genes (DEGs) and identified 2,906 transcripts that were significantly altered. Three in vitro (culture) and three in vivo (in plant) RNAseqs in B. glumae

ORGANISM(S): Burkholderia glumae BGR1

SUBMITTER: Jungwook Park

PROVIDER: E-GEOD-56958 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Understanding pathogenic Burkholderia glumae metabolic and signaling pathways within rice tissues through in vivo transcriptome analyses.

Kim Sunyoung S Park Jungwook J Lee Jongyun J Shin Dongjin D Park Dong-Soo DS Lim Jong-Sung JS Choi Ik-Young IY Seo Young-Su YS

Gene 20140617 1

Burkholderia glumae is a causal agent of rice grain and sheath rot. Similar to other phytopathogens, B. glumae adapts well to the host environment and controls its biology to induce diseases in the host plant; however, its molecular mechanisms are not yet fully understood. To gain a better understating of the actual physiological changes that occur in B. glumae during infection, we analyzed B. glumae transcriptome from infected rice tissues using an RNA-seq technique. To accomplish this, we anal ...[more]

PMID: 24949534

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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

RNAseq analyses of pathogenic Burkholderia glumae under in vitro and in vivo conditions

Publications

Understanding pathogenic Burkholderia glumae metabolic and signaling pathways within rice tissues through in vivo transcriptome analyses.

Similar Datasets

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