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 optima are not fully understood.
• The interplay between taxonomic differences and genomic architecture in shaping expression evolution remains unclear.

Purpose of the Study:

• To compare 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 identify tissue-specific and functional patterns of expression divergence.

Main Methods:

• Comparative analysis of single-copy orthologs in Drosophila and mammalian species pairs.
• Utilized a computational framework to predict expression divergence and species-specific optima.
• Examined tissue-specific and functional patterns of gene expression divergence.

Main Results:

• Drosophila exhibited significantly higher gene expression divergence rates than mammals.
• Nested genes showed no increased likelihood of divergence but larger expression shifts in Drosophila.
• Younger nested genes had higher divergence rates, but shift magnitudes were similar across taxa.
• Distinct taxon- and architecture-specific patterns were observed in reproductive, neural, and metabolic gene functions.

Conclusions:

• Taxonomic context and genome architecture significantly shape gene expression evolution.
• Gene nesting contributes to early regulatory instability rather than large-scale regulatory changes.
• Contrasting patterns of regulatory divergence arise from the interaction of evolutionary history and genomic organization.