Identification of Candidate Genes Associated with the Pileus-Deficient Phenotype in Lentinula edodes Through...

Area of Science:

• Mycology
• Genomics
• Molecular Biology

Background:

• Phenotypic variation is common in mushroom strains, but the underlying genetic mechanisms are unclear.
• Understanding strain-specific traits requires investigating both transcriptional and structural genomic differences.

Purpose of the Study:

• To elucidate molecular mechanisms of phenotypic divergence between Lentinula edodes strains Le_L and Le_S.
• To determine the roles of transcriptional regulation and structural genomic variation in trait differences.

Main Methods:

• Comparative transcriptome analysis to identify differentially expressed genes (DEGs).
• Protein-protein interaction network analysis to map regulatory architectures.
• Ortholog, SNP, INDEL, and presence-absence variation (PAV) analyses.

Main Results:

• 8541 DEGs found, with Le_S upregulated genes linked to protein synthesis and Le_L to metabolism and transport.
• Distinct regulatory networks identified, with conserved hub genes in both strains.
• PAV analysis revealed structural differences in Major Facilitator Superfamily (MFS) transporter genes, absent in Le_S but present and upregulated in Le_L.

Conclusions:

• Structural genomic variation, specifically PAV in transporter genes, is a key driver of phenotypic divergence in Lentinula edodes.
• This study highlights the importance of integrating multi-level genomic analyses to understand fungal strain variation.