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

Assembling high-quality fungal genomes, specifically telomere-to-telomere (T2T) gapless assemblies, often necessitates the integration of multiple sequencing platforms. This requirement poses a limitation on the number of fungal genomes that can feasibly be generated within a single project. Here, we demonstrate that haplotype-aware error correction (HERRO) of Oxford Nanopore simplex reads enables the generation of high-quality assemblies from a single sequencing platform. We present an automated Snakemake workflow that, without manual intervention, produced gapless genome assemblies for industrially relevant strains: <i>Neurospora intermedia</i> NRRL 2884, <i>Trichoderma asperellum</i> TA1, and <i>Aspergillus oryzae</i> CBS 466.91, each achieving complete BUSCO (Benchmarking Universal Single-Copy Orthologs) scores exceeding 98%. Among these, only the <i>T. asperellum</i> assembly yielded a fully telomere-to-telomere gapless genome, while the <i>N. intermedia</i> and <i>A. oryzae</i> assemblies were gapless but near-telomere-to-telomere. Manual curation was required for the mitochondrial genome assembly of <i>N. intermedia</i>.