|VERNYGORA, OKSANA - University Of Kentucky|
|CONGRAINS, CARLOS - University Of Hawaii|
|DUPUIS, JULIAN - University Of Kentucky|
Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/2023
Publication Date: 2/2/2023
Citation: Vernygora, O.V., Congrains, C., Geib, S.M., Dupuis, J.R. 2023. HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources. Molecular Ecology Resources. 23(5):1155-1167. https://doi.org/10.1111/1755-0998.13762.
Interpretive Summary: Multiplexed amplicon sequencing offers a cost-effective and rapid solution for determining the evolutionary relationship of a group of species using genomics. When using amplicon sequencing, the largest challenge is in selecting the most appropriate and informative genetic markers. To improve the ease of marker selection and downstream analysis of phylogenomic amplicon data, we present a flexible and user-friendly tool, HiMAP2, for identifying, visualizing, and filtering phylogenetically informative loci from diverse genomic and transcriptomic resources. To help scientists use this tool, visualization tools have been integrated into a robust analysis pipeline for user-friendly implementation and interpretation, with an outcome of having marker selection be a more informed step in multiplex amplicon phylogenomics.
Technical Abstract: Multiplexed amplicon sequencing offers a cost-effective and rapid solution for phylogenomic studies that include a large number of individuals. Selecting informative genetic markers is a critical initial step in designing such multiplexed amplicon panels, but screening various genomic data and selecting markers that are informative for the question at hand can be laborious. Here, we present a flexible and user-friendly tool, HiMAP2, for identifying, visualizing, and filtering phylogenetically informative loci from diverse genomic and transcriptomic resources. This bioinformatics pipeline includes orthology prediction, exon extraction, and filtering of aligned exon sequences according to user-defined specifications. Additionally, HiMAP2 facilitates exploration of the final filtered exons by incorporating phylogenetic inference of individual exon trees with RAxML-NG as well as the estimation of a species tree using ASTRAL. Finally, results of the marker selection can be visualized and refined with an interactive Bokeh application that can be used to generate publication-quality figures. Source code and user instructions for HiMAP2 are available at https://popphylotools.github.io/HiMAP_v2.