ATCC Genome Portal: Fungal Genome Assembly Improvements and Mitochondrial DNA Recovery

Broadly, the utility of genomic data is constrained by the tools, assumptions, and quality of reference data available at the time the data is generated. As a result, many historical datasets contain biological signals that remain obscured until advances in analytical methods and increased reference representation enable strategic reanalysis.

Here, we perform a comparative analysis of authenticated fungal assemblies from the ATCC Genome Portal against publicly available reference data to assess genome quality, including completeness, genome length, annotation consistency, and phylogenetic classification. This highlights current limitations in fungal genome characterization and identifies opportunities to strengthen dataset quality, improve database design, while preserving the potential for future discovery.

Because mitochondrial genome representations remain inconsistent across public fungal databases, we further evaluate mitochondrial genome availability in a subset of fungal genomes, to explore the potential of mitochondrial DNA (mtDNA) as a complementary resource for phylogenetic inference. Fungal mtDNA exhibits low recombination, diverse inheritance patterns, and mutation rates distinct from the nuclear genome, providing an additional method for improving lineage resolution alongside nuclear‑based classification systems. By revisiting existing genomic datasets, this work demonstrates how preserving data provenance enables iterative refinement of genomic data and can reveal new evolutionary insights.