Genome structure predicts modular transcriptome responses to genetic and environmental conditions

Area of Science:

• Evolutionary biology
• Genomics
• Molecular biology

Background:

• Understanding transcriptome plasticity, robustness, and modularity is key to organismal adaptation.
• Genome architecture significantly influences transcriptome profiles under varying environmental conditions.

Purpose of the Study:

• To investigate how genome architecture shapes transcriptome expression responses to temperature stress in Caenorhabditis briggsae.
• To identify genotype-by-environment interactions (GxE) in gene expression.

Main Methods:

• Quantified gene expression in distinct temperature-adapted genotypes of Caenorhabditis briggsae under chronic temperature stress.
• Analyzed genotype-specific expression changes and identified co-expression modules.
• Examined genomic distributions, functional attributes, and molecular evolution rates of genes within modules.

Main Results:

• 56% of differentially expressed genes showed genotype-specific responses to temperature (GxE).
• Heat stress elicited more genotype-specific responses than cold stress, suggesting distinct genomic architectures.
• Co-expression modules varied in enrichment of genetic, environmental, or interaction effects and showed differential rates of molecular evolution.

Conclusions:

• Transcriptome modularity and genome structure predict evolutionary change.
• Chromosome-scale polymorphism, not individual gene size, drives genetic differences in expression.
• Natural selection acts differently on coding and noncoding sequences, impacting evolutionary trajectories.