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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources
Oksana V Vernygora1, Carlos Congrains2,3, Scott M Geib3
1Department of Entomology, University of Kentucky, Lexington, Kentucky, USA.
Molecular Ecology Resources
|February 2, 2023
Summary
HiMAP2 is a new bioinformatics tool that simplifies selecting informative genetic markers for large-scale phylogenomic studies using multiplexed amplicon sequencing. It efficiently identifies, filters, and visualizes phylogenetic loci from genomic data.
Area of Science:
- Bioinformatics
- Genomics
- Phylogenetics
Background:
- Multiplexed amplicon sequencing is a cost-effective method for large-scale phylogenomic studies.
- Identifying informative genetic markers is crucial but often laborious.
- Existing methods require extensive screening of genomic data.
Purpose of the Study:
- To present HiMAP2, a user-friendly tool for identifying and filtering phylogenetically informative loci.
- To streamline marker selection for multiplexed amplicon panel design.
- To facilitate visualization and refinement of selected markers.
Main Methods:
- HiMAP2 employs orthology prediction and exon extraction from genomic/transcriptomic resources.
- It filters aligned exon sequences based on user-defined criteria.
- Includes phylogenetic inference (raxml-ng) and species tree estimation (astral), with interactive visualization (Bokeh).
Main Results:
- HiMAP2 successfully identifies, filters, and visualizes phylogenetically informative loci.
- The tool integrates orthology prediction, sequence filtering, and phylogenetic analyses.
- An interactive Bokeh application allows for refinement and publication-quality figure generation.
Conclusions:
- HiMAP2 offers a flexible and efficient solution for marker selection in phylogenomic studies.
- The tool reduces the labor involved in screening genomic data for informative markers.
- HiMAP2 enhances the design of multiplexed amplicon panels for evolutionary research.
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