Similar Datasets
Project description:1000 Fungal Genomes
| PRJNA245617 | ENA
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:Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. We also show that antagonism between DNA methylation and histone H2A.Z is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes. Keywords: Epigenetics Examination of DNA methylation and transcription in plant, animal, and fungal genomes, and examination of how H2A.Z deposition relates to both methylation and transcription in puffer fish. Descriptions of the Samples' raw and processed data (provided as supplementary files) can be found in GSE19824_README.txt at the foot of this record.
2010-04-15 | E-GEOD-19824 | biostudies-arrayexpress
Project description:Fungal secondary metabolites represent a rich and largely untapped source for bioactive molecules, including peptides with substantial structural diversity and pharmacological potential. As methods proceed to take a deep dive into fungal genomes, complimentary methods to identify bioactive components are required to keep pace with the expanding fungal repertoire. We developed PepSAVI-MS to expedite the search for natural product bioactive peptides and herein demonstrate proof-of-principle applicability of the pipeline for the discovery of bioactive peptides from fungal secretomes via identification of the antifungal killer toxin KP4 from Ustilago maydis P4. This work opens the door to investigating microbial secretomes with a new lens, and could have broad applications across human health, agriculture, and food safety.
2018-02-19 | PXD006931 | Pride
Project description:Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. We also show that antagonism between DNA methylation and histone H2A.Z is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes. Keywords: Epigenetics
2010-04-15 | GSE19824 | GEO