Augmenting microbial phylogenomic signal with tailored marker gene sets.

Area of Science:

• Microbial genomics
• Bioinformatics
• Phylogenetics

Background:

• Traditional phylogenetic marker gene selection relies on limited, fixed genome collections.
• Metagenome-assembled genomes (MAGs) represent vast microbial diversity but pose challenges due to taxonomic imbalance and non-universal gene families.

Purpose of the Study:

• To introduce TMarSel, an automated tool for tailored marker selection in deep microbial phylogenomics.
• To overcome limitations of traditional marker selection methods for diverse and incomplete genomic data.

Main Methods:

• TMarSel utilizes KEGG and EggNOG annotations for selecting a variable number of gene markers and copies.
• The tool systematically evaluates phylogenetic signals from the entire gene family pool.
• It is designed to be robust against taxonomic imbalance and incomplete genomic data.

Main Results:

• Tailored marker selection using TMarSel significantly improves phylogenetic tree accuracy compared to previous methods.
• This improvement is observed across both whole genomes and metagenome-assembled genomes, including those with missing genes.
• Selected markers are functionally diverse, spanning metabolism, cellular processes, information processing, and core genetic functions.

Conclusions:

• TMarSel offers a flexible and robust solution for marker gene selection in microbial phylogenomics.
• The tool enhances phylogenetic accuracy by leveraging a broader gene set and accommodating data from MAGs.
• Automated, tailored marker selection is crucial for accurately resolving microbial evolutionary relationships.