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RNAseq of Burkholderia to rice root exudates

ABSTRACT: RNAseq analysis of the transcriptomic response of 6 Burkholderia strains to rice root exudates

PROVIDER: PRJEB42574 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5167420.fastq.gz	Fastqsanger.gz
	ERR5168310.fastq.gz	Fastqsanger.gz
	ERR5169500.fastq.gz	Fastqsanger.gz
	ERR5167481.fastq.gz	Fastqsanger.gz
	ERR5169931.fastq.gz	Fastqsanger.gz

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Rhizophagus irregularis gene regulation in response to rice root exudates

Project description:Purpose: The recent publication of the fungal mutualist R. irregularis genome facilitated transcriptomic studies. We here adress the gene regulation of R. irregularis in response to root exudates from rice wild-type and osnope1 (no perception candidate - mutant unable to host arbuscular mycorrhizal fungi) Methods: Spores of R. irregularis were treated with root exudates and collected at 1 hour, 24 hours and 7 days after addition. To monitor fungal gene regulation, control conditions were also prepared at T0, 1h, 24h and 7d. mRNA were sequenced by HiSeq Illumina. Reads were mapped on the Rhizophagus irregularis genome assembly (Gloin1 - Tisserant et al., PNAS, 2013) using CLCworkbench suite. Results: -At 1h, a set of 92 fungal genes were found up-regulated in response to wt root exudates (92), not to osnope1 root exudates, many of them being involved in cell signaling. -At 24h and 7d, numerous genes putatively involved in primary metabolism were up-regulated in response to wt root exudates, not in response to osnope1 root exudates -Several vital genes involved in cell development are repressed in response to osnope1 RE compared to wt RE. Conclusions: these results argue for a high metabolic activity induced by wt root exudates, not by osnope1 root exudates.

2017-02-04 | GSE65595 | GEO

Comparative transcriptomics of Rhizobium mesoamericanum STM3625, Cupriavidus taiwanensis LMG19424 and Burkholderia phymatum STM815 when induced by root exudates of Mimosa pudica

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The responses of CHA0 treated with WT(Col-0) root exudates, Gln and sgn3 myb36 root exudates

Project description:In our previous work, we found that the root exudates of sgn3 myb36 promoted the colonization of CHA0 on roots. Through LC-MS, we identified a large amount of glutamine (Gln) in the root exudates of sgn3 myb36. Therefore, we aim to use RNA-seq to uncover whether the root exudates of sgn3 myb36 and Gln have the same regulatory effects on CHA0. By conducting differential analysis with the CK (CHA0 treated with wild-type root exudates), we hope to identify the specific regulatory mechanisms of sgn3 myb36 and Gln on CHA0.

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Transcriptomics of Bacillus amyloliquefaciens SQR9 to maize root exudates

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Transcriptomics of Bacillus amyloliquefaciens SQR9 to maize root exudates

Project description:Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates. 4 treatments, including 2 blank control (24 h and 48 h-post inoculation, named as 5 and 15, respectively), and 2 treatments with maize root exudates (24 h and 48 h-post inoculation, named as 7 and 17, respectively)

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Project description:Transcription profiles of Bacillus amyloliquefacs FZB42 (cultured to an optical densit of 1.0 or 3.0) in response to root exudates from nutrient-sufficient maize plants and plants starved of nitrogen, phosphorus, potassium or iron.

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Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72.

Project description:Endophytic colonization is a very complex process which is not yet completely understood. Molecules exuded by the plants may act as signals which influence the ability of the microbe to colonize the host or survive in the rhizosphere. Here we investigated whether root exudates of the host might play a role in initiating the endophyte-rice interaction. The whole genome microarray approach was used to investigate the response of the diazotrophic model endophyte, Azoarcus sp. strain BH72, to exudates of O. sativa cv. Nipponbare in order to identify differentially regulated genes. Azoarcus sp. strain BH72 was grown in the presence or absence of root exudates of Oryza sativa cv. Nipponbare for two different time points, and differences in the gene expression profile were monitored.

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Project description:To investigate and compare the influence of root exudates of tomato and maize on Pseudomonas donghuensis P482, we have grown the strain up to a stationary phase in M9 0.4% glucose medium supplemented with maize exudates (Maize), tomato exudates (Tomato) or without supplementation (Control). We then performed differential gene expression analysis, identifying changes in transcriptome profiles between each treatment (Tomato, Maize) and the Control as reference conditions, and between the two treatments.

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Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72.

2012-11-30 | E-GEOD-35187 | biostudies-arrayexpress

Rice Root

Project description:Rice Root Metagenome

| PRJNA964501 | ENA