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Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by insertions of transposable elements

Summary

Scientists sequenced the genome of the prized matsutake mushroom and discovered it has an unusually large genome packed with transposable elements (jumping DNA sequences). These transposable elements act like genetic ‘parasites’ that accumulate over time and actually silence many neighboring genes by preventing them from being expressed. The research shows how mushrooms evolved specialized mechanisms to control these genetic parasites while adapting to living symbiotically with pine tree roots.

Background

Tricholoma matsutake is an ectomycorrhizal fungus that forms symbiotic relationships with pine tree roots and produces highly valued edible mushrooms. Ectomycorrhizal fungi typically have unusually large genomes with high transposable element (TE) content compared to asymbiotic relatives. Understanding the genome structure and transcriptional dynamics of T. matsutake can provide insights into genome size inflation mechanisms.

Objective

This study aimed to sequence and analyze the genome of T. matsutake to understand how transposable element insertions affect genome structure and gene transcription across different developmental stages. The research examined the relationship between TE insertions and transcriptional suppression of neighboring genes and compared genomic features with other ectomycorrhizal fungi.

Results

The T. matsutake genome contained 48.9% repeat elements, with LTR/Gypsy and LTR/Copia being the major classes. Of 702 genes surrounded by TEs, 83.2% showed no transcription at any developmental stage compared to 34.4% overall transcriptional suppression. Evidence of repeat-induced point mutation (RIP) with CpG hypermutation was identified, and IstB-like domains were conserved across mycorrhizal genomes. The genome had reduced carbohydrate-active enzymes typical of ectomycorrhizal fungi.

Conclusion

The T. matsutake genome represents an extreme case of genome expansion driven by transposable element accumulation, with consequent transcriptional suppression of neighboring genes. Genome defense mechanisms including RIP and silencing pathways are active in controlling TE activity. These genomic features reflect the ecological specialization of ectomycorrhizal fungi and provide insights into the evolution of symbiotic fungal genomes.
  • Published in:PLoS One,
  • Study Type:Genomic Analysis,
  • Source: PMID: 31978083, DOI: 10.1371/journal.pone.0227923
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