quercusTOA: Integrated Genomic and Functional Annotations for Nine Oak Species

Nine Quercus genome assemblies are integrated into the quercusTOA resource, which links protein-centric functional annotations with positional genomic data. The resource, created by Fernando Mora-Márquez and last updated in June 2026, provides a standardized framework for evolutionary studies across oak lineages. It includes a relational database and a user-friendly application for tasks like ortholog identification and phylogenetic tree construction.

Use Cases

• Identify cross-species orthologs based on integrated functional annotations and genomic lift-over.
• Perform synteny analysis across oak lineages using the synchronized genomic coordinate framework.
• Construct phylogenetic trees for individual orthologous genes and proteins to study sequence evolution.
• Conduct functional annotation and sequence-based homology searches via the provided quercusTOA-app.

Strengths

• Integrates nine distinct Quercus genome assemblies, providing a multi-species comparative resource.
• Includes a relational database designed to link protein-centric annotations with positional genomic data.
• Offers a user-friendly application (quercusTOA-app) for streamlined database management and bioinformatic tasks.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for large-scale analyses.
• The primary file format is a 258.0 KB PDF, suggesting the dataset is documentation or a summary rather than the raw genomic data itself.

Provenance

Source

Fernando Mora-Márquez via figshare.

Collection Method

Integration of genome assemblies with automated functional annotation (InterProScan, eggNOG-mapper) and comparative genomics via genomic lift-over.

Freshness

Last updated 2026-06-01 05:23:26; freshness should be verified.