Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration

Area of Science:

• Genetics
• Evolutionary Biology
• Genomics

Background:

• Non-recombining genomic regions, such as sex chromosomes, are prone to degenerative mutations.
• Degenerative mutations may lead to differential allele expression, a phenomenon suggested but not extensively tested.
• Sexual antagonism can confound differential expression analysis on sex chromosomes.

Purpose of the Study:

• To investigate the association between specific signatures of sequence degeneration and differential allele expression.
• To utilize the anther-smut fungus *Microbotryum lychnidis-dioicae* as a model system due to its unique chromosomal structure and lack of sexual antagonism.
• To identify specific degenerative mutations linked to altered gene expression in non-recombining regions.

Main Methods:

• Comparative genomics analysis of *Microbotryum lychnidis-dioicae* mating-type chromosomes.
• Identification and categorization of evolutionary strata on mating-type chromosomes.
• Analysis of gene expression levels and sequence degeneration signatures in differentially expressed genes.

Main Results:

• Differentially expressed genes were significantly enriched in the oldest evolutionary strata.
• Several signatures of sequence degeneration were more prevalent in differentially expressed genes compared to non-differentially expressed genes.
• Transposable element insertions upstream of genes and protein-truncating mutations were strongly associated with lower expression levels in differentially expressed allele pairs.

Conclusions:

• A significant association exists between allele degeneration and differential gene expression in non-recombining regions.
• Specific degenerative mutations, including transposable elements and gene truncations, contribute to altered gene expression.
• Findings are relevant for understanding gene regulation in sex determination and mating systems across diverse taxa.