Abstract
Fungal mitochondrial genomes are critical for understanding phylogenetics, evolution, and ecology of the Kingdom Fungi, yet they remain underrepresented in public databases. To address this, we developed a workflow to recover mitochondrial genomes from 12,902 fungal short read sequencing data housed in the Sequence Read Archive (SRA) records, assembling complete circular genomes from 2,695 species. This effort expanded fungal mitochondrial genome diversity by nearly 2.3X particularly in understudied phyla such as Mucoromycota (11X increase) and Zoopagomycota (8X increase). The new dataset contains novel yet undescribed mitochondrial genomes at numerous taxonomic levels, including 15 classes, 64 orders, 178 families, and 544 genera. Taxonomic analysis revealed broad ecological representation among the top-assembled species, including human pathogens (e.g., Cryptococcus tetragattii), plant pathogens (e.g., Melampsora larici-populina), edible mushrooms (e.g., Suillus luteus), and industrial fungi. By leveraging the not yet fully exploited SRA sequencing data, this study fills critical gaps in fungal mitochondrial genomics, tripling the currently known mitochondrial genome diversity of the Kingdom Fungi, and provides an extensive resource for phylogenetic and evolutionary research.
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Code availability
The assembly workflow was implemented in a python script (assembly_workflow.py) passing SRA run accession as input and outputting the assembly contigs and graphs, which are used by GetOrganelle for mitochondrial genome extraction (Methods). The script uses already published tools and explained in the Methods section. The script is available on GitHub at https://github.com/msabrysarhan/fungal_mtDNA.
Data availability
Nucleotide sequence data reported are available in the Third Party Annotation Section of the DDBJ/ENA/GenBank databases under the BioProject PRJNA1367877 and the accession numbers TPA: BK072095-BK074789, and the metadata is available at https://doi.org/10.6084/m9.figshare.28750034.
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Acknowledgements
This work was supported by the “MOC – MultiOmics Centre for Food and Health” project. The MOC project is co-funded by the European Union (European Regional Development Fund – EFRE). Ammar Abdalrahem was supported by a PhD fellowship from the French Ministry of Education and Research (MESR) and by the French Plan Investissement d’Avenir (PIA) Lab of Excellence ARBRE [ANR-11-LABX-0002- 01]. The authors thank the Department of Innovation, Research and University of the Autonomous Province of Bozen/Bolzano, Italy for covering the Open Access publication costs.
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M.S.S. conceived the original idea. M.S.S. and A.A. designed and performed the computational analysis. M.S.S. performed the data visualization and wrote the first draft of the manuscript. M.S.S. and A.A. curated the data for public deposition. F.M. and C.F. edited and revised the manuscript. All authors read and approved the final version of the manuscript.
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Sarhan, M.S., Abdalrahem, A., Maixner, F. et al. De novo assembly of complete circular mitochondrial genomes from 2,695 fungal species.
Sci Data (2025). https://doi.org/10.1038/s41597-025-06447-x
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DOI: https://doi.org/10.1038/s41597-025-06447-x
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