Reconstructing Gene Gains and Losses with BadiRate

Area of Science:

• Evolutionary biology
• Genomics
• Bioinformatics

Background:

• Estimating gene gain and loss is essential for understanding adaptive evolution.
• Previous analyses were limited by the contiguity of genome assemblies.
• Long-read sequencing technologies offer improved resolution for gene family analysis.

Purpose of the Study:

• Introduce BadiRate software for analyzing gene turnover rates.
• Enable high-resolution estimation of gene gains and losses using birth-and-death models.
• Facilitate the study of multigene family variation in evolutionary processes.

Main Methods:

• Implemented birth-and-death stochastic models in BadiRate.
• Utilized maximum likelihood estimation for gene turnover rates.
• Applied phylogenetic species trees to analyze gene family content and evolutionary rates.

Main Results:

• BadiRate estimates gene turnover rates along phylogenetic branches.
• The software infers gene family content at internal nodes and quantifies gene gains/losses.
• Statistical frameworks allow hypothesis testing for accelerated turnover and selection-driven events.

Conclusions:

• BadiRate provides a versatile framework for evolutionary genomics.
• The software enhances the capacity to study gene family evolution with long-read sequencing data.
• Applicability demonstrated through analysis of a hypothetical microbial dataset.