Fungal Genomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1136012 | ENA |
REPOSITORIES: ENA
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Project description:Rhizoctonia solani Kühn is a soilborne basidiomycetous fungus that causes significant damage to many economically important crops. R. solani isolates are classified into 13 Anastomosis Groups (AGs) with interspecific subgroups having distinctive morphology, pathogenicity and wide host range. However, the genetic factors that drive the unique fungal pathology are still not well characterized due to the limited number of available annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 13 R. solani isolates covering 7 AGs and selected subgroups (AG1-IA, AG1-IB, AG1-IC, AG2-2IIIB, AG3-PT, AG3-TB, AG4-HG-I, AG5, AG6, and AG8). Here, we report a pangenome comparative analysis of 13 R. solani isolates covering important groups to elucidate unique and common attributes associated with each isolate, including molecular factors potentially involved in determining AG-specific host preference. Finally, we present the largest repertoire of annotated R. solani genomes, compiled as a comprehensive and user-friendly database, viz. RsolaniDB. Since 7 genomes are reported for the first time, the database stands as a valuable platform for formulating new hypotheses by hosting annotated genomes, with tools for functional enrichment, orthologs and sequence analysis, currently not available with other accessible state-of-the-art platforms hosting Rhizoctonia genome sequences.
2020-10-03 | E-MTAB-9588 | biostudies-arrayexpress
Project description:Coprinellus tropicalis and Coprinellus disseminatus draft fungal genomes Genome sequencing and assembly
| PRJNA509905 | ENA
Project description:CABI fungal endophytes genome sequencing and assembly
| PRJNA786750 | ENA
Project description:Purpose: The recent publication of the fungal mutualist R. irregularis genome facilitated transcriptomic studies. We here wanted to understand the large host range of this fungus, throught its gene regulation in divergent plants Methods: mRNA from Medicago truncatula (legume), Brachypodium distachyon (grass) and Lunularia cruciata (liverwort) in association with R. irregularis were sequenced. Reads were mapped on the genome assembly with the software CLC workbench. Fungal gene expression in the different plants was compared to extra radical hyphae as a control. Results: 529, 486 and 523 R. irregularis gene were highly overexpressed (fold change >5 ; FDR <0,05 and experimental value > l10l) in M. truncatula, B. distachyon and L. cruciata, respectively. Among those genes, 262 were induced in all hosts. qPCR validation on 32 genes supported these results in an extended set of hosts (Zea mays spp parviglumis, Pisum sativum, Marchantia paleacea).
2017-09-29 | GSE67926 | GEO
Project description:MT-2 WGS fungal species isolated from the International Space Station
| PRJNA723004 | ENA
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc