Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast

Area of Science:

• Genomics
• Population Genetics
• Molecular Biology

Background:

• Gene expression links genotype to phenotype, but species-level transcriptome architecture is poorly understood.
• Investigating genetic effects on gene expression across natural populations is crucial.

Purpose of the Study:

• To analyze the pan-transcriptome of ~1,000 yeast natural isolates.
• To identify the role of core and accessory genomes in transcriptome divergence and heritable expression variation.

Main Methods:

• Pan-transcriptome sequencing and analysis of ~1,000 yeast natural isolates.
• Global gene expression pattern analysis integrated with population structure.
• Genome-wide association studies (GWAS) to identify genetic variants influencing gene expression.

Main Results:

• The accessory genome is a major driver of transcriptome divergence between yeast populations.
• Heritable gene expression variation is concentrated in subpopulation-specific signatures, with accessory genes being overrepresented.
• Accessory genes are associated with a higher proportion of variants exhibiting larger effect sizes on gene expression.

Conclusions:

• The accessory genome plays a critical role in shaping the transcriptional landscape within and between yeast populations.
• Understanding the accessory genome is essential for a comprehensive view of gene expression variation and its genetic underpinnings.