A target enrichment probe set for resolving the flagellate land plant tree of life
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Breinholt, Jesse W.1
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Carey, Sarah B.2
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Tiley, George P.3
- Davis, E. Christine2
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Endara, Lorena2
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McDaniel, Stuart F.2
- Neves, Leandro1
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Sessa, Emily B.2
- von Konrat, Matt4
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Fawcett, Susan5
- Ickert-Bond, Stefanie M.6
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Labiak, Paulo H.7
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Larraín, Juan8
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Lehnert, Marcus9
- Lewis, Lily R.2
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Nagalingum, Nathalie S.10
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Patel, Nikisha11
- Rensing, Stefan A.12
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Testo, Weston2
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Vasco, Alejandra13
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Villarreal, Juan Carlos14
- Williams, Evelyn Webb15
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Burleigh, J. Gordon2
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Chantanaorrapint, Sahut16
- Neves, Leandro G.17
- Konrat, Matt4
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Ickert‐Bond, Stefanie M.18
- 1. RAPiD Genomics*
- 2. University of Florida
- 3. Duke University
- 4. Field Museum of Natural History
- 5. University of Vermont
- 6. University of Alaska System
- 7. Federal University of Paraná
- 8. Pontificial Catholic University of Valparaiso
- 9. Martin Luther University Halle-Wittenberg
- 10. California Academy of Sciences
- 11. University of Connecticut
- 12. Philipp University of Marburg
- 13. Botanical Research Institute of Texas
- 14. Université Laval
- 15. Chicago Botanic Garden*
- 16. Prince of Songkla University
- 17. Gainesville Obstetrics & Gynecology
- 18. University of Alaska Fairbanks
Description
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 land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all 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 exons, found in 248 single or low-copy nuclear genes, across flagellate plant lineages. We describe the performance of target enrichment using the probe set across flagellate land plants and demonstrate the potential of the data to resolve relationships among both distantly 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 land plants.
Notes
Details about the dataset and scripts are available in the Breinholt_EtAl_.txt.
Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: 1541506