BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection

Area of Science:

• Evolutionary biology
• Genomics
• Bioinformatics

Background:

• Understanding gene evolution requires analyzing selective forces across lineages.
• The nonsynonymous to synonymous substitution ratio (dN/dS or omega) is a key metric for estimating selection regimes.
• Current tools often exclude non-ubiquitous genes, limiting evolutionary analyses.

Purpose of the Study:

• To present BASE, a novel workflow for inferring gene selection regimes.
• To enable the integration of non-ubiquitous genes in evolutionary studies.
• To facilitate the interpretation of selection pressures in comparative genomics.

Main Methods:

• Leveraging the CodeML framework for selection regime inference.
• Developing a workflow (BASE) to automate analysis of orthologous genes.
• Integrating non-ubiquitous genes into comparative genomic analyses.

Main Results:

• BASE streamlines the inference and interpretation of gene selection regimes.
• The workflow successfully incorporates non-ubiquitous genes, expanding analytical scope.
• Provides a reproducible method for large-scale evolutionary genomics.

Conclusions:

• BASE enhances the study of evolutionary processes by including all orthologous genes.
• Facilitates a more comprehensive understanding of molecular evolution and adaptation.
• Offers a valuable tool for comparative genomics research.