Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1134636 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29777429_1.fastq.gz | Fastqsanger.gz | |||
| SRR29777429_2.fastq.gz | Fastqsanger.gz | |||
| SRR29777430_1.fastq.gz | Fastqsanger.gz | |||
| SRR29777430_2.fastq.gz | Fastqsanger.gz | |||
| SRR29777431_1.fastq.gz | Fastqsanger.gz |
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Project description:Plants are naturally associated with diverse microbial communities, which play significant roles in plant performance, such as growth promotion or fending off pathogens. The roots of Alkanna tinctoria L. are rich in naphthoquinones, particularly the medicinally used chiral compounds alkannin, shikonin and their derivatives. Former studies already have shown that microorganisms may modulate plant metabolism. To further investigate the potential interaction between A. tinctoria and associated microorganisms we performed a greenhouse experiment, in which A. tinctoria plants were grown in the presence of three distinct soil microbiomes. At four defined plant developmental stages we made an in-depth assessment of bacterial and fungal root-associated microbiomes as well as all primary and secondary metabolites. Our results showed that the plant developmental stage was the most important driver influencing the plant metabolite content, revealing peak contents of alkannin/shikonin at the fruiting stage. In contrast, the soil microbiome had the biggest impact on the plant root microbiome. Correlation analyses performed on the measured metabolite content and the abundance of individual bacterial and fungal taxa suggested a dynamic, at times positive or negative relationship between root-associated microorganisms and root metabolism. In particular, the bacterial Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group and the fungal species Penicillium jensenii were found to be positively correlated with higher content of alkannins.
2021-11-28 | ST002021 | MetabolomicsWorkbench
Project description:Insect pathogenic fungus Beauveria bassiana in one of the best studied insect biocontrol fungus, which infects insects by cuticle penetration. After breaking the cuticles, the fungus will propagate in insect hemocoel and kill insect hosts. It has also been found that the mycelia of B. bassiana can penetrate plant tissues to reach insect inside plant, e.g. corn borer (Ostrinia furnacalis), but do not cause damage to plants. The mechanism of fungal physiological plasticity is poorly understood. To accompany our genome sequencing work of B. bassiana strain ARSEF 2860, fungal transcriptional responses to different niches were studied using an Illumina RNA_seq technique. To examine fungal response to insect cuticle, conidia were inoculated on locust hind wings for 24 hours before used for RNA extraction. To evaluate fungal adaptation to insect hemocole, the fifth instar larvae of cotton bollworms were injected with spore suspension and fungal cells isolated by centrifugation in a step gradient buffer. To unveil the mechanism of interaction with plants, the fungus was grown in corn root exudates for 24 hours. After RNA sequencing, around three million tags were acquired for each sample and fungal transcriptional profiles were compared. Unveiling gene differential expression patterns when the insect biocontrol fungus Beauveria bassiana grown in insect hemocoel, corn root exudates and on insect cuticles.
2012-07-10 | E-GEOD-32699 | biostudies-arrayexpress
Project description:Regulated host cell death is part of a plant defense strategy against pathogens but it is also involved in accommodating certain beneficial root microbes. We have identified extracellular metabolites and intracellular metabolic signals that contribute to beneficial root fungal endophyte colonization, and uncovered a conserved cell death mechanism likely co-opted for establishing plant-endophyte symbiosis.
2024-11-17 | GSE209761 | GEO
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 plant signals in the switch from asymbiotic to presymbiotic growth Methods: Spores of R. irregularis were treated with GR24 (strigolactone synthetic analog) and collected at 1 hour, 2 days, 7 days and 14 days after induction. To stimulate the fungus with root exudates, a cellophane membrane allowing molecule exchanges was deposited on in vitro Daucus carotta roots. Spores were spotted on this membrane and collected 14 days after. To monitor fungal gene regulation, control conditions were also prepared and mRNA were sequenced by HiSeq Illumina. Read were mapped on the genome assembly with CLCworkbench Results: At 1 hour, GR24 triggered the overexpression (fold change >2; FDR<0,05) of 123 genes and the repression (fold change < -2; FDR<0,05) of 17 genes. At 2 days, 33 genes were induced, 13 repressed ; at 7 days 106 genes were induced and 13 repressed and at 14 days 19 genes were induced and 10 repressed. Few genes overlap between the different time point. Root exudates induced 251 genes and repressed 63 genes. Few genes were regulated by both GR24 and root exudates. Conclusions: GR24 kinetic showed that fungal gene regulation is sequential, quick and involves hundreds of genes. Among those genes, a chitin synthase, involved either in fungal growth either in symbiotic signal production was strongly induced at 1hour, 7 days and 14 days. As few genes are regulated in response to root exudates and GR24, we propose that other plant signals play a role in ealy steps and trigger fungal gene regulation. Several genes coding for putative secreted peptides were induced in response to these plant signals. These genes might be effectors involved in early plant defense manipulation, then facilitating root entry. Thus, they are good candidates to investigate early steps of plant penetration.
2018-02-01 | GSE67913 | GEO
Project description:Insect pathogenic fungus Beauveria bassiana in one of the best studied insect biocontrol fungus, which infects insects by cuticle penetration. After breaking the cuticles, the fungus will propagate in insect hemocoel and kill insect hosts. It has also been found that the mycelia of B. bassiana can penetrate plant tissues to reach insect inside plant, e.g. corn borer (Ostrinia furnacalis), but do not cause damage to plants. The mechanism of fungal physiological plasticity is poorly understood. To accompany our genome sequencing work of B. bassiana strain ARSEF 2860, fungal transcriptional responses to different niches were studied using an Illumina RNA_seq technique. To examine fungal response to insect cuticle, conidia were inoculated on locust hind wings for 24 hours before used for RNA extraction. To evaluate fungal adaptation to insect hemocole, the fifth instar larvae of cotton bollworms were injected with spore suspension and fungal cells isolated by centrifugation in a step gradient buffer. To unveil the mechanism of interaction with plants, the fungus was grown in corn root exudates for 24 hours. After RNA sequencing, around three million tags were acquired for each sample and fungal transcriptional profiles were compared.
2012-07-10 | GSE32699 | GEO
Project description:Numerous Trichoderma strains are beneficial for plants, promote their growth and confer stress tolerance. A recently described novel Trichoderma strain strongly promotes growth of Arabidopsis thaliana seedlings on media with 50 mM NaCl, while 150 mM NaCl strongly stimulated root colonization and induced salt-stress tolerance in the host without growth promotion. To understand the dynamics of plant-fungus interaction, we examined the secretome from both sides, and revealed a substantial change under different salt regimes, and during co-cultivation. Stress-related proteins, such as fungal Kp4-, WSC- and CFEM-domain-containing proteins, the plant calreticulin and cell-wall modifying enzymes, disappear when the two symbionts are co-cultured under high salt concentrations. More proteins involved in plant and fungal cell wall modifications and the battle of root colonization are found in the co-cultures under salt stress, while the number of plant antioxidant proteins decreased. We identified symbiosis- and salt concentration-specific proteins for both partners. The Arabidopsis PYK10 and a fungal prenylcysteine lyase are only found in the co-culture which promoted plant growth. The comparative analysis of the secretomes suggests that both partners profit from the interaction under salt stress but have to invest more in balancing the symbiosis. We discuss the role of the identified stage- and symbiosis-specific fungal and plant proteins for salt-stress and conditions promoting root colonization and plant growth.
2021-12-15 | PXD028957 | Pride
Project description:Recent sequencing projects have provided deep insight into fungal lifestyle-associated genomic adaptations. Here we report on the 25 Mb genome of the mutualistic root symbiont Piriformospora indica (Sebacinales, Basidiomycota) and provide a global characterization of fungal transcriptional responses associated with the colonization of living and dead roots. Extensive comparative analysis of the P. indica genome with other Basidiomycota and Ascomycota fungi that have diverse lifestyles strategies identified features typically associated with both, biotrophism and saprotrophism. The tightly controlled expression of the lifestyle-associated gene sets during the onset of the symbiosis, revealed by microarrays analysis, argues for a biphasic root colonization strategy of P. indica. Our finding provides a significant advance in understanding development of biotrophic plant symbionts and suggests a series of incremental shifts along the continuum from saprotrophy towards biotrophy in the evolution of mycorrhizal association from decomposer fungi.
2011-10-01 | GSE31266 | GEO
Project description:The root-colonizing fungal endophyte Serendipita indica, formerly known as Piriformospora indica, is well known to promote plant biomass production and stress tolerance of its host plants. Co-cultivation of Arabidopsis thaliana seedlings with the fungus triggers a substantial induction of the growth of the root system. However, the molecular mechanisms by which the fungus promotes plant growth over an extended period of time is still unclear. We here report the comparative analysis of the effect of a mock- and S. indica-infection on wild-type Arabidopsis plants (Col-0) after 2 and 10 days of co-cultivation. Our data provide evidence for the induction of a number of genes that are consistingly induced during the plant–fungus interaction.
2023-09-04 | GSE241902 | GEO