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Updated: May 17, 2025
11:45
Generation of Marked and Markerless Mutants in Model Cyanobacterial Species
Published on: May 29, 2016
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Augmenting microbial phylogenomic signal with tailored marker gene sets.
Henry Secaira-Morocho1,2, Xiaofang Jiang2, Qiyun Zhu1
1Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
Biorxiv : the Preprint Server for Biology
|March 31, 2025
Summary
Selecting tailored phylogenetic marker genes from expanded gene families improves microbial phylogenomics accuracy, especially for metagenome-assembled genomes. This approach enhances phylogenetic tree reconstruction even with incomplete genomic data.
Area of Science:
- Microbial genomics
- Phylogenetics
- Bioinformatics
Background:
- Traditional phylogenetic marker gene selection relies on limited, evenly distributed whole genomes.
- Metagenome-assembled genomes (MAGs) represent vast microbial diversity but often contain novel gene families.
- Existing marker sets struggle with the uneven distribution and unique gene families found in MAGs.
Purpose of the Study:
- To systematically evaluate gene families from KEGG and EggNOG for improved phylogenetic signal in deep microbial phylogenomics.
- To develop a method for selecting accurate phylogenetic markers tailored to specific genomic datasets, including MAGs.
- To introduce a robust software tool for automated marker selection.
Main Methods:
- Systematic evaluation of gene families from KEGG and EggNOG databases.
- Comparative analysis of phylogenetic tree accuracy using traditional vs. expanded, tailored marker sets.
- Testing on simulated and real-world datasets of whole genomes and MAGs.
- Development and application of the TMarSel software tool.
Main Results:
- Markers selected from an expanded pool and tailored to input genomes significantly improve phylogenetic tree accuracy.
- Enhanced marker accuracy is maintained even with incomplete genomic data (missing open reading frames) in MAGs.
- Selected markers encompass diverse functions including metabolism, cellular processes, environmental information processing, replication, translation, and transcription.
Conclusions:
- Tailored marker selection from a broader gene pool enhances microbial phylogenomics, particularly for diverse and incomplete MAGs.
- The TMarSel tool offers automated, flexible, and robust marker selection, overcoming limitations of expert-opinion-based methods.
- This approach advances the accurate reconstruction of microbial evolutionary histories from complex genomic data.
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