Gene Loss Database (GLossDB)

GLossDB centralizes manually curated and validated information on published secondary gene loss events in vertebrate species, enabling searchable access to gene loss mechanisms, supporting evidence, and evolutionary patterns.

Key Features:

• Curated Gene Loss Entries: Each entry compiles the inferred mechanism of gene loss (exon deletion, gene deletion, loss of function mutation) and the type of supporting data (genomic, transcriptomic, single/multiple individual sequence reads, synteny maps).
• Cross-Lineage Information: Entries indicate whether a gene loss event is shared across all lineages within a taxon when available.
• Publication Context: Each entry includes a short excerpt from the original publication to provide biological context.
• Searchable Structure: Information is searchable by species, gene, taxa, or by GO-terms linked to the gene.
• Taxonomic Coverage: The initial release contains 1866 gene loss events across 57 cetacean species and 1321 gene loss events from other vertebrate taxa.

Scientific Applications:

• Evolutionary Pattern Detection: The database facilitates detection of broad evolutionary patterns associated with lineage-specific adaptations, such as aquatic adaptations in cetaceans.
• Downstream Analyses: The structured data supports computational and experimental biologists in downstream evolutionary and functional analyses.
• Gene Loss Mechanism Classification: Researchers can investigate different gene inactivation mechanisms and their genomic or transcriptomic support across species.

Methodology:

Gene loss events were manually curated and validated from published literature, with information structured for searchability by species, gene, taxa, or GO-terms.