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Gapless near Telomer-to-Telomer Assembly of Neurospora intermedia, Aspergillus oryzae, and Trichoderma asperellum from Nanopore Simplex Reads

Summary

Researchers developed a new method to create complete, high-quality genetic maps of fungi using a single affordable sequencing technology from Oxford Nanopore. They created an automated computer program that processes the sequencing data without human intervention and successfully assembled complete genomes for three industrially important fungal species. This breakthrough could make it much easier and cheaper for scientists to study and use fungi for producing medicines, food ingredients, and other useful compounds.

Background

Assembling high-quality fungal genomes to telomere-to-telomere (T2T) completeness typically requires integration of multiple sequencing platforms. Recent advances in error correction methods like HERRO have enabled high-quality assemblies from single sequencing platforms, but applications to industrially relevant fungi remain limited.

Objective

To demonstrate that haplotype-aware error correction (HERRO) of Oxford Nanopore simplex reads enables generation of high-quality, gapless fungal genome assemblies from a single sequencing platform, and to present an automated Snakemake workflow for producing such assemblies.

Results

The workflow produced gapless genome assemblies for Neurospora intermedia NRRL 2884, Aspergillus oryzae CBS 466.91, and Trichoderma asperellum TA1, each with BUSCO scores exceeding 98%. Only T. asperellum achieved a fully telomere-to-telomere assembly; the other two were gapless near-T2T genomes. The workflow successfully identified biosynthetic gene clusters, carbohydrate-active enzymes, and telomeric regions.

Conclusion

HERRO-corrected Nanopore simplex reads can generate high-quality fungal T2T or near-T2T assemblies without complementary sequencing platforms. The automated Snakemake workflow provides a reproducible, scalable approach for fungal genomics research, supporting applications in species identification, drug discovery, industrial strain development, and comparative genomics.
  • Published in:Journal of Fungi,
  • Study Type:Methods Development Study,
  • Source: PMID: 41149891
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