A likelihood ratio test for changes in homeolog expression bias.

Area of Science:

• Evolutionary biology
• Genomics
• Molecular biology

Background:

• Gene duplication is a key driver of evolutionary innovation and biological diversity.
• Duplicate genes can evolve new functions, often through altered expression patterns.
• Analyzing expression patterns of duplicate genes provides insights into their evolutionary trajectories.

Purpose of the Study:

• To develop and validate a statistical method for analyzing expression ratios of duplicate genes.
• To investigate homeolog expression bias in allotetraploid monkeyflower (Mimulus luteus).

Main Methods:

• Development of a likelihood ratio test for comparing expression ratios of duplicate genes across two conditions.
• Application of the test to RNA-sequencing data from Mimulus luteus leaves and petals.
• Assessment of test sensitivity to expression bias and comparison with alternative methods.

Main Results:

• A novel likelihood ratio test was developed for analyzing homeolog expression patterns.
• The test was applied to 1448 homeologous gene pairs in Mimulus luteus.
• The method demonstrated superior performance compared to existing approaches.

Conclusions:

• The developed likelihood ratio test is a robust and efficient tool for detecting changes in homeolog expression bias.
• This method offers a transparent and easily implementable approach for evolutionary and functional genomics studies.
• The test is broadly applicable to analyzing expression ratio changes between any two genes in any two conditions.