Using the MaizeGDB genome browser to evaluate gene model annotation quality and gain functional insights

Résumé fourni par la source

MaizeGDB’s genome browsers provide a suite of tools, data, and resources to enable users to evaluate gene model annotation quality and gain functional insights into maize genomics. MaizeGDB now has a set of Syntenome tracks for B73 version 5 that offer whole-genome alignments with other grasses and their lifted gene models to enable comparative analyses that support gene model validation and highlight conserved and diverged regions. These tracks include unmethylated regions, aligned protein fragments from the Maize Peptide Atlas, and confidence scores from protein structure predictions. Along with over 300 gene expression tracks, these datasets support a robust framework for both inter-species and cross-species comparisons. Additionally, protein structure alignments from AlphaFold and ESMFold, alongside full proteome alignments from over 20 species via UniProt and Phytozome, lend further validation and functional context. Alternative annotations from NCBI, Helixer, and Mikado offer confirmatory evidence, while transcriptional start site predictions from CAGE data refine the 5’ untranslated regions of gene model annotations. Functional insights are further enriched by curated annotations, including UniProt descriptions, Gene Ontology terms, AI-based predictions, and transcription factor annotations from Grassius. Pangenome and pan-gene annotations from the NAM founder genomes and other high-quality maize assemblies enable users to explore structural and functional diversity across maize lineages. Over 600 epigenetic and DNA-binding datasets, such as transcription factor binding sites, open chromatin regions, and histone modifications, add additional layers of regulatory context. The genome browser has over one thousand total tracks that also integrate tools for visualizing SNPs, INDELs, and large-scale variations, alongside forward genetics resources like UniformMu, BonnMu, and Ac/Ds insertions. Tight integration with gene model pages, BLAST tools, SNPVersity (a variant viewer), and PanEffect (a variant effect viewer) ensures seamless navigation and analysis. Together, these resources allow users to critically evaluate gene models, uncover functional insights, and advance maize genetics and genomics research. As a member of the AgBioData Consortium, MaizeGDB is committed to upholding FAIR (Findable, Accessible, Interoperable, and Reusable) data standards to support robust, open, and collaborative research.

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