A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae
Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing o...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2014-02-01
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| Series: | Applications in Plant Sciences |
| Subjects: | |
| Online Access: | http://www.bioone.org/doi/full/10.3732/apps.1300085 |
| _version_ | 1818587202249031680 |
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| author | Jennifer R. Mandel Rebecca B. Dikow Vicki A. Funk Rishi R. Masalia S. Evan Staton Alex Kozik Richard W. Michelmore Loren H. Rieseberg John M. Burke |
| author_facet | Jennifer R. Mandel Rebecca B. Dikow Vicki A. Funk Rishi R. Masalia S. Evan Staton Alex Kozik Richard W. Michelmore Loren H. Rieseberg John M. Burke |
| author_sort | Jennifer R. Mandel |
| collection | DOAJ |
| description | Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses.
Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family.
Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families. |
| first_indexed | 2024-12-16T09:05:06Z |
| format | Article |
| id | doaj.art-826fad51355245beac50a6de9d08752d |
| institution | Directory Open Access Journal |
| issn | 2168-0450 |
| language | English |
| last_indexed | 2024-12-16T09:05:06Z |
| publishDate | 2014-02-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj.art-826fad51355245beac50a6de9d08752d2022-12-21T22:37:05ZengWileyApplications in Plant Sciences2168-04502014-02-0122130008510.3732/apps.1300085A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the CompositaeJennifer R. Mandel0Rebecca B. Dikow1Vicki A. Funk2Rishi R. Masalia3S. Evan Staton4Alex Kozik5Richard W. Michelmore6Loren H. Rieseberg7John M. Burke8Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152 USACenter for Conservation and Evolutionary Genetics, National Zoological Park and Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USADepartment of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USADepartment of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USADepartment of Genetics, Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602 USAThe Genome Center, University of California, Davis, California 95616 USAThe Genome Center, University of California, Davis, California 95616 USADepartment of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4 CanadaDepartment of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USAPremise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.http://www.bioone.org/doi/full/10.3732/apps.1300085base treeconservedexon capturenext-generation sequencingorthologsphylogenomics |
| spellingShingle | Jennifer R. Mandel Rebecca B. Dikow Vicki A. Funk Rishi R. Masalia S. Evan Staton Alex Kozik Richard W. Michelmore Loren H. Rieseberg John M. Burke A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae Applications in Plant Sciences base tree conserved exon capture next-generation sequencing orthologs phylogenomics |
| title | A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae |
| title_full | A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae |
| title_fullStr | A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae |
| title_full_unstemmed | A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae |
| title_short | A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae |
| title_sort | target enrichment method for gathering phylogenetic information from hundreds of loci an example from the compositae |
| topic | base tree conserved exon capture next-generation sequencing orthologs phylogenomics |
| url | http://www.bioone.org/doi/full/10.3732/apps.1300085 |
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