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

PREMISE New sequencing technologies facilitate the generation of large‐scale molecular data sets 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, includ...

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Published inApplications in plant sciences Vol. 9; no. 1; pp. e11406 - n/a
Main Authors Breinholt, Jesse W., Carey, Sarah B., Tiley, George P., Davis, E. Christine, Endara, Lorena, McDaniel, Stuart F., Neves, Leandro G., Sessa, Emily B., Konrat, Matt, Chantanaorrapint, Sahut, Fawcett, Susan, Ickert‐Bond, Stefanie M., Labiak, Paulo H., Larraín, Juan, Lehnert, Marcus, Lewis, Lily R., Nagalingum, Nathalie S., Patel, Nikisha, Rensing, Stefan A., Testo, Weston, Vasco, Alejandra, Villarreal, Juan Carlos, Williams, Evelyn Webb, Burleigh, J. Gordon
Format Journal Article
LanguageEnglish
Published United States John Wiley & Sons, Inc 01.01.2021
John Wiley and Sons Inc
Wiley
Subjects
Application
Bryophyta
Deoxyribonucleic acid
Design
DNA
DNA probes
Evolution
Exons
Ferns
flagellate plants
Flowers & plants
Gene expression
Genes
Genetic testing
Genomes
Genomics
Gymnosperms
Mosses
next‐generation sequencing
nuclear loci
Nucleotide sequence
Phylogenetics
phylogenomics
Phylogeny
Plant sciences
target enrichment
transcriptome
Transcriptomes
United States > US
nuclear loci
target enrichment
next‐generation sequencing
phylogenomics
flagellate plants
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Abstract PREMISE New sequencing technologies facilitate the generation of large‐scale molecular data sets 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 We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single‐copy or low‐copy nuclear genes across flagellate plant lineages. RESULTS Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. 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.
AbstractList PREMISENew sequencing technologies facilitate the generation of large‐scale molecular data sets 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.METHODSWe leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single‐copy or low‐copy nuclear genes across flagellate plant lineages.RESULTSOur results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics.CONCLUSIONSA 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.
PREMISE: New sequencing technologies facilitate the generation of large‐scale molecular data sets 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: We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single‐copy or low‐copy nuclear genes across flagellate plant lineages. RESULTS: Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. 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.
New sequencing technologies facilitate the generation of large-scale molecular data sets 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.PREMISENew sequencing technologies facilitate the generation of large-scale molecular data sets 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.We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages.METHODSWe leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages.Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics.RESULTSOur results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics.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.CONCLUSIONSA 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.
PREMISE New sequencing technologies facilitate the generation of large‐scale molecular data sets 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 We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single‐copy or low‐copy nuclear genes across flagellate plant lineages. RESULTS Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. 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.
New sequencing technologies facilitate the generation of large-scale molecular data sets 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. We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages. Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. 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.
Author Burleigh, J. Gordon
Davis, E. Christine
Carey, Sarah B.
Fawcett, Susan
Ickert‐Bond, Stefanie M.
Testo, Weston
Chantanaorrapint, Sahut
Labiak, Paulo H.
Nagalingum, Nathalie S.
Williams, Evelyn Webb
Endara, Lorena
Lehnert, Marcus
Patel, Nikisha
Breinholt, Jesse W.
McDaniel, Stuart F.
Sessa, Emily B.
Villarreal, Juan Carlos
Larraín, Juan
Lewis, Lily R.
Tiley, George P.
Neves, Leandro G.
Vasco, Alejandra
Konrat, Matt
Rensing, Stefan A.
AuthorAffiliation 4 Department of Biology Duke University Durham North Carolina USA
13 Department of Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA
16 Department of Biology Laval University Québec City Québec Canada
12 California Academy of Sciences San Francisco California USA
7 Pringle Herbarium Department of Plant Biology University of Vermont Burlington Vermont USA
1 RAPiD Genomics Gainesville Florida USA
10 Instituto de Biología Pontificia Universidad Católica de Valparaíso Valparaíso Chile
8 Department of Wildlife and Biology and UA Museum of the North University of Alaska Fairbanks Fairbanks Alaska USA
6 Department of Biology Faculty of Science Prince of Songkla University Songkhla Thailand
15 Botanical Research Institute of Texas Fort Worth Texas USA
3 Department of Biology University of Florida Gainesville Florida USA
5 Department of Research and Education The Field Museum Chicago Illinois USA
17 Chicago Botanic Garden Glencoe Illinois USA
14 Faculty of Biology University
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/33552748$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Copyright 2021 Breinholt et al. is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America
2021 Breinholt et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.
2021. This work is published under http://creativecommons.org/licenses/by-nc-nd/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Copyright_xml – notice: 2021 Breinholt et al. is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America
– notice: 2021 Breinholt et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.
– notice: 2021. This work is published under http://creativecommons.org/licenses/by-nc-nd/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Issue 1
Keywords nuclear loci
target enrichment
next‐generation sequencing
phylogenomics
flagellate plants
Language English
License Attribution-NonCommercial-NoDerivs
2021 Breinholt et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.
This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
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Snippet PREMISE New sequencing technologies facilitate the generation of large‐scale molecular data sets for constructing the plant tree of life. We describe a new...
New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set...
PREMISENew sequencing technologies facilitate the generation of large‐scale molecular data sets for constructing the plant tree of life. We describe a new...
PREMISE: New sequencing technologies facilitate the generation of large‐scale molecular data sets for constructing the plant tree of life. We describe a new...
PREMISE New sequencing technologies facilitate the generation of large‐scale molecular data sets for constructing the plant tree of life. We describe a new...
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SubjectTerms Application
Bryophyta
Deoxyribonucleic acid
Design
DNA
DNA probes
Evolution
Exons
Ferns
flagellate plants
Flowers & plants
Gene expression
Genes
Genetic testing
Genomes
Genomics
Gymnosperms
Mosses
next‐generation sequencing
nuclear loci
Nucleotide sequence
Phylogenetics
phylogenomics
Phylogeny
Plant sciences
target enrichment
transcriptome
Transcriptomes
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Title A target enrichment probe set for resolving the flagellate land plant tree of life
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