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quercusTOA: integrating functional annotations and comparative genomics across oak lineages
Fernando Mora-Márquez1, Mikel Hurtado2,3, Unai López de Heredia1
1GI en Desarrollo de Especies y Comunidades Leñosas (WooSP), Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain.
Frontiers in Bioinformatics
|June 17, 2026
Summary
We developed quercusTOA, a genomic resource integrating nine oak (Quercus) genome assemblies. This database links functional annotations with genomic data, aiding evolutionary and functional studies in Quercus species.
Area of Science:
- Genomics
- Bioinformatics
- Forest Ecology
Background:
- Oak (Quercus) species are vital to Northern Hemisphere forests.
- Integrating diverse oak genomic data presents significant challenges.
Purpose of the Study:
- To create a unified genomic and functional resource for Quercus species.
- To facilitate comparative genomics and evolutionary analyses across multiple oak assemblies.
Main Methods:
- Integrated nine Quercus genome assemblies into a relational database.
- Employed automated functional annotation (InterProScan, eggNOG-mapper) and comparative genomics (genomic lift-over).
- Developed the quercusTOA-app for user-friendly data access and bioinformatic tasks.
Main Results:
- Established a database linking protein annotations with positional genomic data.
- Enabled cross-species ortholog identification and synteny analysis.
- Facilitated functional annotation, homology searches, multiple sequence alignments, and phylogenetic tree construction.
Conclusions:
- quercusTOA offers a standardized framework for evolutionary and functional genomics in Quercus.
- The resource ensures consistent genomic coordinate synchronization across the genus.
- Facilitates in-depth study of sequence evolution and gene function in oaks.
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