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The Neurospora crassa Pangenome: A Robust Framework for Population-Scale Analysis and Structural Variant Discovery
Huawei Tan1, Sihai Yang1, Xiaohui Zhang1
1School of Life Sciences, Nanjing University, Nanjing 210023, China.
Journal of Fungi (Basel, Switzerland)
|July 27, 2026
Summary
This study reveals two main genetic lineages in Neurospora crassa, with differing genome sizes and transposable element (TE) levels. A new pangenome framework aids in understanding fungal adaptation and stress response.
Area of Science:
- * Genomics and Molecular Evolution
- * Mycology and Fungal Genetics
Background:
- * Limited reference genomes hinder understanding of Neurospora crassa's genetic diversity.
- * High genetic diversity exists within this widely distributed ascomycete.
Purpose of the Study:
- * To create a comprehensive pangenome for Neurospora crassa.
- * To investigate molecular evolution and genetic variation across N. crassa strains.
- * To establish a framework for identifying adaptive evolution in filamentous fungi.
Main Methods:
- * Integrated functional annotation of the FGSC2225 genome.
- * Comparative genomic analysis of N. crassa strains.
- * De novo assembly of 72 high-quality draft genomes for pangenome construction.
- * Phylogenetic analysis of gene families (HET-domain, heat shock TFs, bZIP, CYP450).
Main Results:
- * Identified two primary N. crassa lineages (Clade A and Clade B), with Clade A having larger genomes.
- * FGSC2225 genome proportions mirrored FGSC2489, but with higher transposable element (TE) levels compared to Sordaria macrospora.
- * Demonstrated varying conservation and presence/absence variation in key gene families across lineages.
Conclusions:
- * The developed pangenome provides a framework for detecting rapid adaptive evolution in filamentous fungi.
- * This methodology can identify crucial factors for fungal stress response and virulence.
- * Addresses limitations of current genomic resources for N. crassa research.
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