Taxonomic context and genomic architecture jointly shape expression divergence across animals

Area of Science:

• Evolutionary biology
• Genomics
• Molecular biology

Background:

• Gene expression divergence drives phenotypic variation, but factors influencing regulatory evolution are not fully understood.
• The interplay between taxonomic differences and genomic architecture in shaping expression evolution remains unclear.

Purpose of the Study:

• To quantify taxon-specific rates and magnitudes of gene expression divergence between Drosophila and mammals.
• To assess the impact of genome architecture, specifically gene nesting, on expression evolution.
• To investigate tissue-specific and functional patterns of expression divergence.

Main Methods:

• Analysis of single-copy orthologs in Drosophila and mammalian species pairs.
• Development of a computational framework to predict expression divergence and optima.
• Comparative analysis of nested versus unnested genes regarding divergence rates and expression shifts.

Main Results:

• Drosophila exhibits significantly higher gene expression divergence rates than mammals.
• Nested genes did not show higher divergence likelihood but exhibited larger expression optima shifts in Drosophila.
• Younger nested genes had higher divergence rates, suggesting early regulatory instability without large magnitude changes.

Conclusions:

• Taxonomic context and genome architecture independently shape gene expression evolution.
• Distinct patterns of regulatory divergence exist across tissues and functional categories.
• Gene nesting influences early regulatory instability, particularly in Drosophila, affecting specific gene functions like metabolism.