Quantifying Transcriptome Turnover on Phylogenies by Modeling Gene Expression as a Binary Trait

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• Gene expression changes are crucial for phenotypic evolution, driving interest in transcriptome evolution.
• Traditional models treat gene expression as continuous, overlooking qualitative transitions.
• Organ-specific gene expression patterns represent a key area for evolutionary study.

Purpose of the Study:

• To develop novel Bayesian inference techniques for studying the evolutionary turnover of organ-specific transcriptomes.
• To define and analyze instances where orthologous genes gain or lose expression in a specific organ.
• To investigate the evolutionary dynamics of gene expression in male reproductive organs across Drosophila species.

Main Methods:

• Development of new Bayesian inference techniques for evolutionary transcriptome analysis.
• Discretization of gene expression states by estimating expression probabilities per gene, organ, and species.
• Phylogenetic modeling of correlated transcriptome evolution across multiple organs, applied to 11 Drosophila melanogaster group species.

Main Results:

• Analysis of testes and accessory gland transcriptomes in 11 Drosophila species revealed significant gene expression gains and losses.
• The developed phylogenetic model identified numerous instances of orthologous genes gaining or losing expression in specific organs.
• Accelerated transcriptome turnover was observed in the two studied reproductive organs, occurring on distinct evolutionary branches.

Conclusions:

• The new Bayesian methods provide a robust framework for studying qualitative changes in organ-specific transcriptomes.
• Gene expression turnover is a common evolutionary process in organ development and function.
• Distinct evolutionary trajectories of transcriptome turnover exist even between closely related organs.