Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms.

Area of Science:

• Evolutionary biology
• Genomics
• Systems biology

Background:

• Gene regulation underlies species-specific traits.
• Comparative genomics offers insights into evolutionary divergence.
• Gene coexpression networks map functional gene relationships.

Purpose of the Study:

• To investigate the evolution of gene regulation across species.
• To quantify the conservation of gene activity over evolutionary time.
• To understand the role of gene regulation in cell identity and diversification.

Main Methods:

• Comparative analysis of gene coexpression networks from 37 species.
• Quantification of gene activity conservation across evolutionary time.
• Assessment of conservation across different orthology prediction algorithms.
• Evaluation with reference to cell- and tissue-specificity.

Main Results:

• Gene coexpression patterns are conserved across evolutionary time.
• Ancient genes show conserved coexpression but differential expression levels across cell types.
• Differential regulation of ancient gene programs contributes to transcriptional cell identity.

Conclusions:

• Differential gene regulation is a key driver of cell identity.
• This mechanism plays a role in cell diversification in both animals and plants.
• Comparative gene coexpression network analysis is a powerful framework for evolutionary studies.