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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene profiling during symbiosis between the actinorhizal tree Casuarina glauca and the actinobacteria Frankia CcI3

ABSTRACT: Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in C. glauca. Symbiosis between C. glauca and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition. Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for C. glauca, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent.

ORGANISM(S): Casuarina glauca

SUBMITTER: Valérie HOCHER

PROVIDER: E-GEOD-24158 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene profiling during symbiosis between the actinorhizal tree Alnus glutinosa and the actinobacteria Frankia alni ACN14

Project description:Alnus glutinosa belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in A. glutinosa. Symbiosis between A. glutinosa and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition. Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for A. glutinosa, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent

2011-04-11 | E-GEOD-24153 | biostudies-arrayexpress

Gene profiling during symbiosis between the actinorhizal tree Casuarina glauca and the actinobacteria Frankia CcI3

Project description:Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in C. glauca. Symbiosis between C. glauca and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition.

2011-04-07 | GSE24158 | GEO

Gene profiling during symbiosis between the actinorhizal tree Casuarina glauca and the actinobacteria Frankia CcI3 after treatment with 1-naphtoxy acetic acid, an auxin influx inhibitor.

Project description:Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to study the role of the plant growth regulator auxin during actinorhizal symbiosis and to identify key plant genes that are involved in auxin signaling during symbiosis in C. glauca. Symbiosis between C. glauca and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen (N2) which favors the induction of nitrogen fixing symbiosis. For auxin role study, plant were treated with 25µM 1-naphtoxy acetic acid (1-NOA) all along nodulation time. Nodule were harvested 3 weeks after inoculation. For this study we considered two stages: - 21 days old nodules obtained on plants not treated with 1-NOA (control condition) - 21 days old nodules obtained on plants supplemented with 25µM of 1-NOA. Three biological replicates were used for each condition, however due to non valid staistics, two of the replicates (one for control condition, one for treated condition were removed.

2014-12-31 | GSE55582 | GEO

Gene profiling in arbuscular mycorrhizal symbiosis between the actinorhizal tree Casuarina glauca and the fungus Glomus intraradices.

Project description:Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. They can also develop arbuscular mycorrhizae (AM) while associated with Glomeromycota fungi. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program in AM and to identify new key plant genes involved in endosymbioses. C. glauca plants were grown in hydroponics then transferred to pots with or without spores of Glomus intraradices and watered with low phosphate solution to enhance mycorrhization. For this study we considered two stages: - a stage where plants were inoculated with G. intraradices, roots were harvested 8 weeks after inoculation with the G. intraradices. AM structures were present. - a stage where plants were not inoculated, roots were harvested at the same time as the inoculated roots , this is our control condition. AM structures were absent. Three biological replicates were used for each condition. Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for C. glauca, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent.

2012-10-22 | E-GEOD-36676 | biostudies-arrayexpress

Genes differentially expressed in wild-type Medicago truncatula plants during nodulation

Project description:We used an Affymetrix oligonucleotide microarray consisting of 9,935 tentative consensus (TC)sequences, which are based on cDNA libraries (Mitra et al., 2004 [PMID:15220482]). We examined gene expression of wild-type M. truncatula plants after inoculation with wild-type S. meliloti at 1 d, 4 d, 7d, 14 d, and 21 d. We chose these time points because they span the range of development of the Rhizobium-legume symbiosis, from initiation of the interaction through nitrogen fixation. The gene expression data for the 1-day time point (Mitra et al., 2004 [PMID 15220482]) and the other time points was previously published (Starker el al., 2006 [PMID 16407449]). Three or five independent biological replicates were performed at each time point (1, 4, 7, 14 and 21 days after treatment) and each treatment (buffer and wild-type bacteria).

2011-03-26 | E-GEOD-28173 | biostudies-arrayexpress

Gene profiling during symbiosis between the actinorhizal tree Alnus glutinosa and the actinobacteria Frankia alni ACN14

2011-04-11 | GSE24153 | GEO

Transcription profiling of soybean nodulation by Bradyrhizobium japonicum

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2008-02-04 | E-GEOD-10340 | biostudies-arrayexpress

affy_ams_maize-Cell wall maize mutant during arbuscular mycorrhizal symbiosis

Project description:affy_ams_maize - aafy_ams_maize - Main objectives of this study: - role of plant cell wall during AM symbiosis - regulation pattern during AM symbiosis - understanding of the original mycorrhizal phenotype of bm4 - search of candidate-genes to study AM symbiosis-After 7 days in phytochambers, plantlets were transplanted in 2L of humidified bedrock with 3000 spores for inoculation conditions or without spore for mock conditions then plants have grown in greenhouse. Maize roots have been sampled 7 weeks post-inoculation and freezed in liquid nitrogen then stocked at -80M-BM-0C. Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturerM-bM-^@M-^Ys instructions. Keywords: treated vs untreated comparison 8 arrays - maize

2011-05-03 | E-GEOD-22950 | biostudies-arrayexpress

affy_med_2011_09-Analysis of Medicago truncatula root transcriptome in response to mycorrhization by Glomus intraradices under phosphate and nitrogen limitation

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2013-01-01 | E-GEOD-38847 | biostudies-arrayexpress

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2023-03-11 | PXD038609 | Pride

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