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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of Azospirillum lipoferum 4B during its interaction with rice roots

ABSTRACT: Investigation of whole genome gene expression level changes in a Azospirillum lipoferum 4B associated to artificial roots, Oryza sativa japonica cv. Cigalon roots and Oryza sativa japonica cv. Nipponbare roots, compared to the strain grown in liquid culture. For each of the four condition, two replicates were analysed on an A. lipoferum 4B whole genome expression array designed by Roche Nimblegen, Inc. (Madison, WI, USA), based on the genome sequence (Wisniewski-DyM-CM-) et al. 2011), as follows: two replicates of 5 probes (length, 60 nucleotides) per gene, covering 6,242 genes and using a total of 62,178 probes.

ORGANISM(S): Azospirillum lipoferum 4B

SUBMITTER: BenoM-CM-.t DROGUE

PROVIDER: E-GEOD-42450 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome analysis of Azospirillum lipoferum 4B during its interaction with rice roots

Project description:Investigation of whole genome gene expression level changes in a Azospirillum lipoferum 4B associated to artificial roots, Oryza sativa japonica cv. Cigalon roots and Oryza sativa japonica cv. Nipponbare roots, compared to the strain grown in liquid culture.

2014-01-01 | GSE42450 | GEO

Rice roots: Non-colonized (sterile) control vs. colonized with Azoarcus olearius BH72

Project description:Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post inoculation with Azoarcus olearius BH72, the goal is to understand the transcriptomic response of rice roots to colonization by bacterial endophyte

2019-09-01 | GSE136707 | GEO

Rice roots: Non-colonized (sterile) control vs. infected with Xanthomonas oryzae pv. oryzae strain PXO99 (Xan)

Project description:Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post infection with Xanthomonas oryzae pv. oryzae strain PXO99 , the goal is to understand the transcriptomic response of rice roots to colonization by bacterial pathogen

2019-09-01 | GSE136706 | GEO

Plant root transcriptome profiling of Azospirillum-rice cooperation

2014-12-22 | GSE59137 | GEO

Plant root transcriptome profiling of Azospirillum-rice cooperation

Project description:Cooperation involving Plant Growth-Promoting Rhizobacteria results in improvements of plant growth and health. While pathogenic and symbiotic interactions are known to induce transcriptional changes for genes related to plant defense and development, little is known about the impact of phytostimulating rhizobacteria on plant gene expression. In this context, this study aimed at identifying genes significantly regulated in rice roots upon Azospirillum inoculation, considering possible favored interaction between a strain and its original host cultivar. Genome-wide analyses of root gene expression of Oryza sativa japonica cultivars Cigalon and Nipponbare were performed, by using microarrays, seven days post inoculation with A. lipoferum 4B (isolated from Cigalon roots) or Azospirillum sp. B510 (isolated from Nipponbare) and compared to the respective non-inoculated condition. For each of the four condition, three replicates were analysed on an oligo microarray produced by NimbleGenTM (Madison, WI, USA). The microarray was derived of the one previously described in Yuan et al. 2005 . This microarray is composed of about 385,000 60mer probes selected for their GC content, Tm and number of cycles needed to synthesize the oligo. This chip contains 90,000 probes representing 45,000 genes (two probes per gene) of rice Oryza sativa ssp. japonica, based on the TIGR rice genome annotation version 3.1 genes (Chaparro et al. 2007) and 201 691 oligomers corresponding to previously described copies of LTR retrotranposons available on the retrOryza database (www.retroryza.fr). Probes represent 1,000 bp of the LTR-retrotransposon flanking regions at the 3M-bM-^@M-^Y and 5M-bM-^@M-^Y side. The oligonucleotides have been designed at the 3M-bM-^@M-^Y end of the genes to detect the readings of reverse transcriptase. On the other hand, the LTR-retrotransposons are represented throughout their length at the rate of a probe every 500 bp.

2014-12-22 | E-GEOD-59137 | biostudies-arrayexpress

The RNA-seq analysis of rice roots colonized by the endophytic bacterium Azoarcus olearius BH72 after one-, three- and seven-days post inoculation and after three days of boosted colonization.

Project description:Purpose: Transcriptional profiling of Oryza sativa japonica Nipponbare roots after one, three and seven days post inoculation with Azoarcus olearius BH72 (vs. non-inoculated controls) to understand the changes in transcriptomic response of rice roots to colonization by bacterial endophyte at initial stages of interaction; Additional set-up was included in which bacterial growth was boosted (through increasing 20-times carbon source - malic acid in the plant's hydroponic medium) to study rice roots transcriptome during enhanced colonization by the endophyte after three days post inoculation. Methods: Rice root mRNA profiles after one day, three days (including additional set-ups for boosted colonization), and seven days post inoculation with Azoarcus olearius BH72 and corresponding non-inoculated controls were generated by RNA sequencing, in triplicates, using Illumina NextSeq 500. Raw reads were then filtered, trimmed (PHRED > 33) and mapped onto IRGSP-1 version of Oryza sativa ssp. japonica cv. Nipponbare genome using CLC Genomics Workbench 8.5.1 (Qiagen, Germany). Expression of 17 selected genes was confirmed via RT-qPCR. Results: Using the RNA-Seq technology we obtained transcriptomic data from 24 sequencing libraries, with an average 46,181,160 clean reads per library, of which 87% or more were mapped onto the Oryza sativa ssp. japonica cv. Nipponbare IRGSP-1.0 genome (Fig. S3). We considered genes as differentially regulated (DEG) that exhibited at least 1.5-fold-change in expression level between Azo-colonized and non-colonized roots and FDR<0.05. Conclusions: Bacteria appeared to short-circuit the initial root defense responses for a compatible interaction during endophytic establishment, involving previously unknown putative rice candidate genes.

2021-09-01 | GSE174616 | GEO

A phosphoproteomic landscape of rice (Oryza sativa L.) tissues

Project description:Here, we first reported the construction of a phosphoproteomic landscape of 6 tissues, including callus, leaves, roots, shoot meristem (SM), young panicles (YP) and mature panicles (MP), from Nipponbare (Oryza sativa ssp. japonica). By employing a non-gel, quantitative phosphoproteomic approach, a total of 4792 phosphopeptides from 2657 phosphoproteins were identified, which were found to be differentially phosphorylated among tissues.

2018-04-11 | PXD005241 | Pride

Characterize novel lncRNAs responding to stresses in Oryza sativa at transcriptional and post-transcriptional levels

Project description:We performed poly(A)+, poly(A)-, nuclear, small RNA-seq analysis on Oryza sativa japonica WT plants.

2018-06-13 | GSE86215 | GEO

Oryza sativa Japonica cultivar:Kitaake Transcriptome or Gene expression

Project description:RNA-seq of Oryza sativa Japonica cultivar Kitaake

2015-02-11 | E-MTAB-4326 | biostudies-arrayexpress

Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae strain BLS354

Project description:We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease. Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354 with three biological replicates compared to three replicates of mock inoculated O. sativa as the control.

2016-07-07 | E-GEOD-75131 | biostudies-arrayexpress

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