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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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quercusTOA: integrating functional annotations and comparative genomics across oak lineages.

Fernando Mora-Márquez¹, Mikel Hurtado^2,3, 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.

Keywords:

Quercus SQLite database comparative genomics forest genetics functional annotation genomic lift-over orthology

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Published on: May 9, 2017

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.