HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources

Oksana V. Vernygora; Carlos Congrains; Scott M. Geib; Julian R. Dupuis

doi:10.1111/1755-0998.13762

HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources

Oksana V. Vernygora, Carlos Congrains, Scott M. Geib, Julian R. Dupuis

Research output: Contribution to journal › Article › peer-review

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://github.com/popphylotools/HiMAP_v2.

Original language	English
Pages (from-to)	1155-1167
Number of pages	13
Journal	Molecular Ecology Resources
Volume	23
Issue number	5
DOIs	https://doi.org/10.1111/1755-0998.13762
State	Published - Jul 2023

Bibliographical note

Publisher Copyright:
© 2023 John Wiley & Sons Ltd.

Funding

We thank Forest Bremer for assistance with software development and Alana Alexander, Anita Lerch and an anonymous reviewer for comments on earlier drafts of the manuscript. We thank the University of Kentucky Center for Computational Sciences and Information Technology Services Research Computing for their support and use of the Lipscomb Compute Cluster and associated research computing resources. This research was supported by USDA-NIFA HATCH to JRD (Project KY008091) and United States Department of Agriculture (USDA) Plant Protection Act 7721 (Project AP20PPQS&T00C154). The US Department of Agriculture, Agricultural Research Service is an equal opportunity/affirmative action employer, and all agency services are available without discrimination. All opinions expressed in this paper are the authors' and do not necessarily reflect the policies and views of USDA. We thank Forest Bremer for assistance with software development and Alana Alexander, Anita Lerch and an anonymous reviewer for comments on earlier drafts of the manuscript. We thank the University of Kentucky Center for Computational Sciences and Information Technology Services Research Computing for their support and use of the Lipscomb Compute Cluster and associated research computing resources. This research was supported by USDA‐NIFA HATCH to JRD (Project KY008091) and United States Department of Agriculture (USDA) Plant Protection Act 7721 (Project AP20PPQS&T00C154). The US Department of Agriculture, Agricultural Research Service is an equal opportunity/affirmative action employer, and all agency services are available without discrimination. All opinions expressed in this paper are the authors' and do not necessarily reflect the policies and views of USDA.

Funders	Funder number
USDA‐NIFA HATCH
University of Kentucky Medical Center
U.S. Department of Agriculture	AP20PPQS, T00C154
National Institute of Food and Agriculture	KY008091

Keywords

comparative genomics
genome
phylogenetic informativeness
targeted amplicon design
transcriptome

ASJC Scopus subject areas

Biotechnology
Ecology, Evolution, Behavior and Systematics
Genetics

Access to Document

10.1111/1755-0998.13762

Cite this

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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://github.com/popphylotools/HiMAP_v2.",

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HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources

Abstract

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

Access to Document

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