Documentation
The MycoVirome Online Platform is a curated dataset and discovery workflow for Botrytis cinerea mycoviruses.
Overview
This website provides a curated dataset of mycovirus genomes reported from Botrytis cinerea strains collected worldwide. Our goal is to merge fragmented information across public repositories and publications into a single, consistent, and reusable reference platform that supports Botrytis cinerea as a biological system for comparative analyses of mycoviruses and reproducible virus discovery in fungal systems.
FAIR principles
This dataset is curated following the FAIR principles:
- Findable: each entry includes unique identifiers (virus accession (IDs)) adopted form the original source, and registered or indexed in the searchable database.
- Accessible: the dataset is made available through this web interface and links back to the original primary sources whenever possible. Any updates are reported through the GitHub repository as a standardized communication open protocol.
- Interoperable: curated metadata follow consistent naming that follows FAIR principles, and include references to other relevant metadata for knowledge representation, enabling downstream reuse in scripts and workflows.
- Reusable: the platform provides documentation, provenance links, scripts, analysis workflow links, and outputs designed to be accurate and to support replication and extension by other sources. The main goal is to be released with a clear, accessible data usage license, associated with detailed provenance, and to meet domain-relevant community standards.
Note: We aim to maintain consistency, but the dataset inherits limitations from source records (incomplete metadata, inconsistent naming, and variable levels of annotation). Curatorial decisions are documented whenever possible, and the dataset will continue to be refined. Updates can be followed through the repository.
Dataset scope
The curated dataset focuses on mycovirus genomes isolated or identified from Botrytis cinerea strains worldwide. We compile and curate genome sequences and metadata like taxonomy, ecological variables, and isolate-level information, in detail, including (when available):
- Viral taxonomy: Species, Genus, Family, genome type.
- Virus accession identifiers, database source, and genome sequence descriptors
- Genome configuration (e.g., segmentation and genome type)
- Isolate id and year (where reported)
- Links to source databases and/or literature
We intended that users use the platform for both exploratory browsing and downstream analysis (e.g., phylogenetics, comparative genomics, and diversity summaries).
Interactive analytics
To support exploration of the current dataset, we provide interactive charts and summary views that help users navigate the high diversity of B. cinerea-associated mycoviruses. We designed the analytics to make it easier to:
- Inspect genome metadata
- Explore temporal trends in virus accessions (when year metadata is available)
- Summarize diversity across genome configurations and taxonomic groups (families and related clades)
We intended to provide these plots as entry points for exploration; users are encouraged to download or reuse the curated table for custom analyses.
Virus discovery and classification workflow
In addition to the dataset, we link to a reproducible workflow for virus discovery and classification from fungal meta(transcriptomic) datasets. We designed the workflow to support:
- Virus discovery from fungal metatranscriptomes
- Classification of identified viral contigs using phylogenetics
- Generation of reference alignments and phylogenetic trees for viral families
- Placement/visualization of newly identified viral contigs relative to curated references
Outputs and visualization
The workflow generates intermediate and final outputs that are linked back to this platform, including:
- Alignments of curated reference sequences
- Viral family phylogenetic trees
- Visualization support to inspect alignments and interpret the phylogenetic position of viral contigs
These visual outputs help interpret novel or divergent viral contigs discovered in fungal meta(transcriptomic) datasets.
Issues
We welcome corrections and contributions (e.g., missing accessions, improved metadata, taxonomic updates, and new analytical views). Please open an issue or start a discussion on the GitHub repository. GitHub.