Ontology highlight
ABSTRACT:
PROVIDER: PRJNA769432 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16242200_1.fastq.gz | Fastqsanger.gz | |||
| SRR16242200_2.fastq.gz | Fastqsanger.gz | |||
| SRR16242201_1.fastq.gz | Fastqsanger.gz | |||
| SRR16242201_2.fastq.gz | Fastqsanger.gz | |||
| SRR16242202_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 40 |
Similar Datasets
Project description:Illumina HiSeq2000 technology was used to generate mRNA profiles from Vaccinium myrtillus mycorrhizal and non-mycorrhizal roots with or without Cadmium treatment. 150bp reads were generated and aligned to a Vaccinium myrtillus de novo assembly as reference using CLC Genomics Workbench 8.
2020-02-12 | GSE119554 | GEO
Project description:Illumina HiSeq2000 technology was used to generate mRNA profiles from Oidiodendron maius free-living mycelium and Vaccinium myrtillus mycorrhizal roots with or without Cadmium treatment. 150bp reads were generated and aligned to the O.maius reference transcripts using CLC Genomics Workbench 8
2020-02-12 | GSE119266 | GEO
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress
Project description:High ambient temperature regulated the plant systemic response to the beneficial endophytic fungus Serendipita indica. Most plants in nature establish symbiotic associations with endophytic fungi in soil. Beneficial endophytic fungi induce a systemic response in the aboveground parts of the host plant, thus promoting the growth and fitness of host plants. Meanwhile, temperature elevation from climate change widely affects global plant biodiversity as well as crop quality and yield. Over the past decades, great progresses have been made in the response of plants to high ambient temperature and to symbiosis with endophytic fungi. However, little is known about their synergistic effect on host plants. The endophytic fungus Serendipita indica colonizes the roots of a wide range of plants, including Arabidopsis. Based on the Arabidopsis-S. indica symbiosis experimental system, we analyzed the synergistic effect of high ambient temperature and endophytic fungal symbiosis on host plants. By transcriptome analysis, we found that DNA replication-related genes were significantly upregulated during the systemic response of Arabidopsis aboveground parts to S. indica colonization. Plant hormones, such as jasmonic acid (JA) and ethylene (ET), play important roles in plant growth and systemic responses. We found that high ambient temperature repressed the JA and ET signaling pathways of Arabidopsis aboveground parts during the systemic response to S. indica colonization in roots. Meanwhile, PIF4 is the central hub transcription factor controlling plant thermosensory growth under high ambient temperature in Arabidopsis. PIF4 is also involving JA and/or ET signaling pathway. We found that PIF4 target genes overlapped with many differentially expressed genes (DEGs) during the systemic response, and further showed that the growth promotion efficiency of S. indica on the pif4 mutant was higher than that on the wild type plants.
2022-02-26 | GSE197325 | GEO
Project description:Roots of Arabidopsis thaliana do not engage in symbiotic association with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors having diverse lifestyles and retained diverse repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.
2021-11-03 | GSE169629 | GEO
Project description:Conidial germination marks the beginning of the fungal life cycle, and understanding the genes associated with conidial germination provides insights into fungal pathogenicity and host interactions. Here, we use comparative transcriptomics to demonstrate the transcriptional similarities and differences during conidial germination and initial colony establishment in a plant pathogenic and an endophytic fungus, Fusarium graminearum and M. anisopliae, respectively. We compared the transcriptomes of F. graminearum and M. anisopliae across four stages of conidial germination: fresh conidia, polar growth, hyphal extension, and either first hyphal branching (on medium) or appressorium formation (on barley). F. graminearum exhibited a higher upregulation of CAZyme, specialized metabolite and effector genes compared to M. anisopliae during interaction with the host, particularly in the appressorium stage, reflecting its pathogenic nature. The appressorium structures formed when M. anisopliae conidia germinated on the host. The transcriptome analysis revealed that the fungus produced reduced transcript levels of CAZyme and specialized metabolite genes reflecting a less aggressive host penetration approach. The candidate genes associated with IAA synthesis were upregulated in M. anisopliae during the appressorium stage, supporting its endophytic lifestyle and suggests that the fungus uses a phytohormone based strategy to interact with plant hosts. Collectively, our findings expand the transcriptome resources and provide valuable insights into the gene networks involved in conidial germination and initiation of infection in pathogenic versus endophytic fungus.
2024-11-05 | GSE277787 | GEO
Project description:Conidial germination marks the beginning of the fungal life cycle, and understanding the genes associated with conidial germination provides insights into fungal pathogenicity and host interactions. Here, we use comparative transcriptomics to demonstrate the transcriptional similarities and differences during conidial germination and initial colony establishment in a plant pathogenic and an endophytic fungus, Fusarium graminearum and M. anisopliae, respectively. We compared the transcriptomes of F. graminearum and M. anisopliae across four stages of conidial germination: fresh conidia, polar growth, hyphal extension, and either first hyphal branching (on medium) or appressorium formation (on barley). F. graminearum exhibited a higher upregulation of CAZyme, specialized metabolite and effector genes compared to M. anisopliae during interaction with the host, particularly in the appressorium stage, reflecting its pathogenic nature. The appressorium structures formed when M. anisopliae conidia germinated on the host. The transcriptome analysis revealed that the fungus produced reduced transcript levels of CAZyme and specialized metabolite genes reflecting a less aggressive host penetration approach. The candidate genes associated with IAA synthesis were upregulated in M. anisopliae during the appressorium stage, supporting its endophytic lifestyle and suggests that the fungus uses a phytohormone based strategy to interact with plant hosts. Collectively, our findings expand the transcriptome resources and provide valuable insights into the gene networks involved in conidial germination and initiation of infection in pathogenic versus endophytic fungus.
2024-11-05 | GSE277627 | GEO