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<p>Intracellular parasitic fungi such as microsporidia and rozellids exhibit extreme genome reduction, complicating assembly from uncultured samples after whole genome amplification. Multiple displacement amplification (MDA) generates uneven coverage, resulting in fragmented metagenome-assembled genomes (MAGs). We present a Snakemake-based pipeline integrating assembly, binning, and BUSCO-based phylogenomics. The pipeline achieves about 45% BUSCO completeness for microsporidian MAGs, consistent with biological gene loss. This workflow enables accurate reconstruction of reduced genomes for evolutionary studies.</p>

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Optimized pipeline for assembly of intracellular parasitic fungi genomes from MDA data

  • 期刊论文

  • 发表日期：

    2025年11月4日

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  • Mikhail Rayko,
  • Elena Nassonova

摘要

Intracellular parasitic fungi such as microsporidia and rozellids exhibit extreme genome reduction, complicating assembly from uncultured samples after whole genome amplification. Multiple displacement amplification (MDA) generates uneven coverage, resulting in fragmented metagenome-assembled genomes (MAGs). We present a Snakemake-based pipeline integrating assembly, binning, and BUSCO-based phylogenomics. The pipeline achieves about 45% BUSCO completeness for microsporidian MAGs, consistent with biological gene loss. This workflow enables accurate reconstruction of reduced genomes for evolutionary studies.