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

Summary

Scientists developed an automated computer workflow that can assemble complete fungal genomes using data from a single type of DNA sequencer. They tested this method on three industrially important fungi and successfully created high-quality, gap-free genome maps for all three. This breakthrough means researchers can now generate high-quality fungal genome sequences faster and more cheaply than before, which will help improve our understanding of these organisms.

Background

Assembling high-quality fungal genomes to telomere-to-telomere (T2T) completeness typically requires combining multiple sequencing platforms, which limits the number of fungal genomes that can feasibly be generated. Recent advances in error correction methods like HERRO have enabled T2T assemblies from single Nanopore sequencing platforms.

Objective

To demonstrate that haplotype-aware error correction (HERRO) of Oxford Nanopore simplex reads enables generation of high-quality gapless or near-gapless fungal genome assemblies from a single sequencing platform. The study presents an automated Snakemake workflow for producing complete fungal genomes without manual intervention.

Results

The workflow produced gapless genome assemblies for Neurospora intermedia NRRL 2884 and Aspergillus oryzae CBS 466.91 (near-T2T) and Trichoderma asperellum TA1 (fully T2T), all with BUSCO scores exceeding 98%. The assemblies identified 8790, 13042, and 9805 genes respectively, along with numerous biosynthetic gene clusters and carbohydrate-active enzymes.

Conclusion

HERRO-corrected Nanopore simplex data can generate high-quality fungal T2T or near-T2T assemblies without requiring multiple sequencing platforms. The automated Snakemake workflow provides a scalable, reproducible solution for fungal genome assembly, potentially increasing the quality of fungal genomes available in public databases.
  • Published in:Journal of Fungi,
  • Study Type:Methods Development Study,
  • Source: 10.3390/jof11100701, PMID: 41149891
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