Atmospheric fungal diversity of grapevine
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ABSTRACT:
PROVIDER: PRJNA427126 | ENA |
REPOSITORIES: ENA
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Project description:Fungal Diversity in Root Restricted grapevine
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Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from grapevine wood infected by a fungal pathogen in the presence of a root biological control agent. One of the goals was to obtain molecular data about the fungus pathogen (Phaeomoniella chlamydospora) during grapevine wood infection. Grapevine pathogen-infected wood mRNA profiles of 2-month-old plantlets (14 days post infection) were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed by TopHat followed by Cufflinks. qRTaPCR validation was performed using SYBR Green assays. Using an optimized data analysis workflow, we mapped sequence reads to the grapevine genome (build IGGP 12x) and identified pathogen transcripts. RNAseq analyses, using a ribosomal RNA depletion technology for library preparation, provided identification of genes expressed by P. chlamydospora during infection: as for genes related to effector biosynthesis enzymes, carbohydrate-active enzymes and transcription regulators involved in known regulation pathways in fungi. Insights about P. oligandrum modulation of grapevine infection by this pathogen were also found. Our study represents the first detailed analysis of grapevine wood infection by a fungal pathogen generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive evaluation of mRNA content within grapevine wood tissue. We conclude that RNA-seq based transcriptome characterization would permit the dissection of complex biologic interactions.
2015-10-23 | E-MTAB-3966 | biostudies-arrayexpress
Project description:Outdoor atmospheric PM2.5 Raw sequence reads
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Project description:Greenland Ice Sheet fungal diversity Raw sequence reads (ITS2)
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Project description:Svalbard glaciers fungal diversity Raw sequence reads (ITS2)
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Project description:Purpose: Lasiodiplodia theobromae is a pathogenic fungus causing Botryosphaeria dieback in grapevine. Heat and drought stress was suggested to promote the disease incidence in recent years, therefore we decided to evaluate the effect of heat on in vitro experiment, adding grapevine wood to simulate the environment in the trunk during in field infection. Methods: Fungal mRNA was extracted from mycellium collected after 49 hours of growth without stress in the presence of GW (GW_noHS) or in its absence (VS_noHS). Some mRNA were extracted form mycellium collected 10 min after stress (1 hour at 42 C) both in the presence of GW (GW_HS) or in its absence (VS_HS). The cDNA and sequenciation was done according with Illumina HiSeq 2500 recomendations by triplicate. Paired end reads (100bp) were used for de novo assembly through Trinity. Transdecoder was used to predict ORFs. The transcripts functional annotatio was done through BlastX and Blast2GO. Bowtie2 was used to map the reads for each sample to the previously assembled transcritome, a homemade Perl script was used to count the mapped reads and edgeR was employed for differential expression and statistical analysis. Results: Seventy million reads were asembled to produce 19,860 transcripts, from those 15,981 were predicted to codify for ORFs. Thirty-five % of transcripts did not have any homologue in NCBI NR database, most of those also did not were predicted to codify for ORFs. With the remainning 38 % of transcripts the functional annotation was obtained. Around 90% of reads for each sample were mapped to the de novo assembled transcriptome. Around 2339 genes were differentially expressed when comparing GW_HS vs GW_noHS or vs VS_noHS and GW_noHS vs VS_noHS and VS_HS vs VS_noHS. Hierarchical clustering with functional enrichment were used to predict metabolic pathways with differential regulation. In silico prediction were then verified with RT-qPCR showing linear correlation (r2=0.87) in in vitro experiment. Then trough in planta fungal gene expression helps to verify that phenolic metabolism is important for colonization in grapevine. Conclusion: A model for fungal response to HS in the presence of GW was proposed. This correspond to the first work to identify nucleotide sequences, measure gene expression and propose pathogenicity factors important for disease establishment in grapevine.
2016-12-10 | GSE75978 | GEO
Project description:Fungal entomopathogens like Beauveria bassiana (Bals.) Vuill. (Ascomycota: Hypocreales) are known as antagonist of insects with multiple functional and ecological roles and have attracted increased attention as biocontrol agents in integrated pest management programs. A microarray analysis was performed to work out fundamental aspects of genes involved in the interaction between grapevine and the endophytic fungus B. bassiana. The results indicate an up-regulation of diverse defense-related genes in grapevine as a response to a treatment with B. bassiana
2019-12-31 | GSE132311 | GEO