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A target enrichment probe set for resolving the flagellate plant tree of life

Jesse W. Breinholt, Sarah B. Carey, George P. Tiley, E. Christine Davis, Lorena Endara, Stuart F. McDaniel, Leandro G. Neves, Emily B. Sessa, Matt von Konrat, Sahut Chantanaorrapint, Susan Fawcett, Stefanie M. Ickert-Bond, Paulo H. Labiak, Juan Larraín, Marcus Lehnert, Lily R. Lewis, Nathalie S. Nagalingum, Nikisha Patel, Stefan A. Rensing, Weston Testo, Alejandra Vasco, Juan Carlos Villarreal, Evelyn Webb Williams, J. Gordon Burleigh
doi: https://doi.org/10.1101/2020.05.29.124081
Jesse W. Breinholt
1RAPiD Genomics, Gainesville, FL, USA
2Intermountain Heathcare, Intermountain Precision Genomics, Saint George, UT, USA
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Sarah B. Carey
3Department of Biology, University of Florida, Gainesville, FL, USA
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George P. Tiley
3Department of Biology, University of Florida, Gainesville, FL, USA
4Department of Biology, Duke University, Durham, NC, USA
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E. Christine Davis
3Department of Biology, University of Florida, Gainesville, FL, USA
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Lorena Endara
3Department of Biology, University of Florida, Gainesville, FL, USA
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Stuart F. McDaniel
3Department of Biology, University of Florida, Gainesville, FL, USA
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Leandro G. Neves
1RAPiD Genomics, Gainesville, FL, USA
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Emily B. Sessa
3Department of Biology, University of Florida, Gainesville, FL, USA
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Matt von Konrat
5Department of Research and Education, The Field Museum, Chicago, IL, USA
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Sahut Chantanaorrapint
6Department of Biology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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Susan Fawcett
7Pringle Herbarium, Department of Plant Biology, University of Vermont, Burlington, VT, USA
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Stefanie M. Ickert-Bond
8Department of Wildlife and Biology & UA Museum of the North, University of Alaska Fairbanks (UAF), Fairbanks, AK, USA
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Paulo H. Labiak
9Dept. Botanica, Universidade Federal do Parana, Curitiba-PR, Brazil
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Juan Larraín
10Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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Marcus Lehnert
11Geobotany & Botanical Garden, Herbarium, Martin Luther University Halle-Wittenberg, Halle, Germany
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Lily R. Lewis
3Department of Biology, University of Florida, Gainesville, FL, USA
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Nathalie S. Nagalingum
12California Academy of Sciences, San Francisco, USA
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Nikisha Patel
13Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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Stefan A. Rensing
14Faculty of Biology, University of Marburg, Marburg, Germany
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Weston Testo
3Department of Biology, University of Florida, Gainesville, FL, USA
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Alejandra Vasco
15Botanical Research Institute of Texas, Fort Worth, TX, USA
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Juan Carlos Villarreal
16Department of Biology, Laval University, Quebec City, Quebec, Canada
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Evelyn Webb Williams
17Chicago Botanic Garden, Glencoe, IL, USA
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J. Gordon Burleigh
3Department of Biology, University of Florida, Gainesville, FL, USA
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  • For correspondence: gburleigh@ufl.edu
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ABSTRACT

Premise of the study New sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate plants, comprising hornworts, liverworts, mosses, lycophytes, ferns, and gymnosperms.

Methods and Results We leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target enrichment sequencing of 451 nuclear exons and non-coding flanking regions across flagellate plant lineages. We describe the performance of target enrichment using the probe set across flagellate plants and demonstrate the potential of the data to resolve relationships among both ancient and closely related taxa.

Conclusions A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate plants.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 30, 2020.
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A target enrichment probe set for resolving the flagellate plant tree of life
Jesse W. Breinholt, Sarah B. Carey, George P. Tiley, E. Christine Davis, Lorena Endara, Stuart F. McDaniel, Leandro G. Neves, Emily B. Sessa, Matt von Konrat, Sahut Chantanaorrapint, Susan Fawcett, Stefanie M. Ickert-Bond, Paulo H. Labiak, Juan Larraín, Marcus Lehnert, Lily R. Lewis, Nathalie S. Nagalingum, Nikisha Patel, Stefan A. Rensing, Weston Testo, Alejandra Vasco, Juan Carlos Villarreal, Evelyn Webb Williams, J. Gordon Burleigh
bioRxiv 2020.05.29.124081; doi: https://doi.org/10.1101/2020.05.29.124081
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A target enrichment probe set for resolving the flagellate plant tree of life
Jesse W. Breinholt, Sarah B. Carey, George P. Tiley, E. Christine Davis, Lorena Endara, Stuart F. McDaniel, Leandro G. Neves, Emily B. Sessa, Matt von Konrat, Sahut Chantanaorrapint, Susan Fawcett, Stefanie M. Ickert-Bond, Paulo H. Labiak, Juan Larraín, Marcus Lehnert, Lily R. Lewis, Nathalie S. Nagalingum, Nikisha Patel, Stefan A. Rensing, Weston Testo, Alejandra Vasco, Juan Carlos Villarreal, Evelyn Webb Williams, J. Gordon Burleigh
bioRxiv 2020.05.29.124081; doi: https://doi.org/10.1101/2020.05.29.124081

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