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Root associated fungus metagenome

ABSTRACT: Arbuscular mycorrhizal fungi communities in the roots of the invasive Nicotiana glauca and co-occurring native plants

PROVIDER: PRJNA521301 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8561440_1.fastq.gz	Fastqsanger.gz
	SRR8561440_2.fastq.gz	Fastqsanger.gz
	SRR8561450_1.fastq.gz	Fastqsanger.gz
	SRR8561450_2.fastq.gz	Fastqsanger.gz
	SRR8561460_1.fastq.gz	Fastqsanger.gz

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root metagenome

Project description:Arbuscular mycorrhizal fungi communities in the roots of the invasive Nicotiana glauca and native plants under dry and wet conditions

| PRJNA1279009 | ENA

Gene expression data from arbuscular mycorrhizal and phosphate-treated Medicago truncatula roots.

Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression in Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on whole mycorrhizal roots. We used GeneChips to detail the global programme of gene expression in response to colonization by arbuscular mycorrhizal fungi and in response to a treatment with phosphate and identified genes differentially expressed during this process. Medicago truncatula roots were harvested at 28 days post inoculation with the two different arbuscular mycorrhizal fungi Glomus intraradices (Gi-Myc) and Glomus mosseae (Gm-Myc) under low phosphate conditions (20 µM phosphate) or after a 28 days treatment with 2 mM phosphate in the absence of arbuscular mycorrhizal fungi (2mM-P). As a control, uninfected roots grown under low phosphate conditions (20 µM phosphate) were used (20miM-P). Three biological replicates consisting of pools of five roots were used for RNA extraction and hybridization on Affymetrix GeneChips.

2011-10-28 | E-GEOD-32208 | biostudies-arrayexpress

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

Small RNA sequencing in tomato roots with and without Rhizophagus irregularis

Project description:Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control.

2016-07-20 | GSE76204 | GEO

Gene expression data from arbuscular mycorrhizal and phosphate-treated Medicago truncatula roots.

2011-10-29 | GSE32208 | GEO

A roadmap of cell-type specific gene expression during late stages of the arbuscular mycorrhiza symbiosis

Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel cell-type specific gene expression during late stages of Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on laser-microdissected cells. We used Medicago GeneChips to detail the cell-type specific programme of gene expression in late stages of colonization by arbuscular mycorrhizal fungi and identified genes differentially expressed during these stages. Medicago truncatula Gaertn M-bM-^@M-^XJemalongM-bM-^@M-^Y genotype A17 plantlets were grown in the climate chamber. Plants grown for the collection of root cortical cells containing arbuscules (ARB), root cortical cells from mycorrhizal roots (CMR), and root epidermal cells from mycorrhizal roots (EPI) were mycorrhized after 2 weeks with Glomus intraradices and mycorrhizal roots were harvested at around 21 days post inoculation (dpi).

2013-04-28 | E-GEOD-42747 | biostudies-arrayexpress

Small RNA sequencing in tomato roots with and without Rhizophagus irregularis

2016-07-20 | E-GEOD-76204 | biostudies-arrayexpress

Effects of arbuscular mycorrhizal symibiosis on gene expression in the foxtail millet roots

Project description:To investigate the involvement of arbuscular mycorrhizal symbiosis in the moleular regulation in foxtail millet roots and the effects of genetic variation on AMS-mediated molecular regulation, we isolated total RNA from the roots of 3 different landraces for comprehensive transcriptomic analysis. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different landraces (Hanevalval, TT8, ICE36) after 6-week mock or arbuscular mycorrhizal fungi treatments.

2022-10-20 | GSE213843 | GEO

GRAS transcription factors activated in arbuscule-containing cells of Medicago truncatula

Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition by the host. To unravel the role of the AM-specific GRAS transcription factors MtGras1 and MtRam1, we performed genome-wide transcriptome profiling in RNAi-mediated MtGras1 knockdown and MtRam1 (ram1-1) mutant roots. Specifically, we used GeneChip Medicago Transcriptome Assays to identify genes differentially regulated in mycorrhizal MtGras1 knockdown or MtRam1 (ram1-1) mutant roots in comparison to control roots.

2019-02-27 | GSE108867 | GEO

Large-scale transcriptomics provides insights on the mycorrhizal symbiosis of the Mediterranean orchid Limodorum abortivum in nature

Project description:The study of orchid mycorrhizal interactions is particularly complex because of the peculiar life cycle of these plants and their diverse trophic strategies. Here, large-scale transcriptomics has been applied to investigate gene expression in the mycorrhizal roots of the terrestrial mixotrophic orchid Limodorum abortivum under natural conditions. Our results provide new insights into the mechanisms underlying plant-fungus interactions in orchids and in particular on the plant responses to the mycorrhizal symbiont(s) in adult roots. Comparison with gene expression in mycorrhizal roots of another orchid species, Oeceoclades maculata, suggests that amino acids may represent the main nitrogen source in both protocorms and adult orchids, at least for mixotrophic species. The upregulation, in mycorrhizal L. abortivum roots, of some symbiotic molecular marker genes identified in mycorrhizal roots from other orchids as well as in arbuscular mycorrhiza, suggests a common plant core of genes in endomycorrhizal symbioses. Further efforts will be required to understand whether the specificities of orchid mycorrhiza depend on fine-tuned regulation of these common components, or whether specific additional genes are involved.

2021-01-31 | GSE159700 | GEO

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