HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment
Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of...
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| Published in | Applications in plant sciences Vol. 4; no. 7 |
|---|---|
| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Botanical Society of America
01.07.2016
John Wiley & Sons, Inc |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper. |
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| AbstractList | Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper. Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of highthroughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a userfriendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae).Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper. Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper. Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high‐throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user‐friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper. Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae).PREMISE OF THE STUDYUsing sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae).HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.METHODS AND RESULTSHybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.CONCLUSIONSHybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper. |
| Author | Medina, Rafael Wickett, Norman J Gardner, Elliot M Shaw, A. Jonathan Goffinet, Bernard Johnson, Matthew G Liu, Yang Zerega, Nyree J. C |
| Author_xml | – sequence: 1 givenname: Matthew G surname: Johnson fullname: Johnson, Matthew G organization: Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, Illinois 60022 USA – sequence: 2 givenname: Elliot M surname: Gardner fullname: Gardner, Elliot M organization: Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208 USA – sequence: 3 givenname: Yang surname: Liu fullname: Liu, Yang organization: Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut 06269 USA – sequence: 4 givenname: Rafael surname: Medina fullname: Medina, Rafael organization: Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut 06269 USA – sequence: 5 givenname: Bernard surname: Goffinet fullname: Goffinet, Bernard organization: Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut 06269 USA – sequence: 6 givenname: A. Jonathan surname: Shaw fullname: Shaw, A. Jonathan organization: Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708 USA – sequence: 7 givenname: Nyree J. C surname: Zerega fullname: Zerega, Nyree J. C organization: Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208 USA – sequence: 8 givenname: Norman J surname: Wickett fullname: Wickett, Norman J organization: Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208 USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27437175$$D View this record in MEDLINE/PubMed |
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| Notes | www.datadryad.org www.artocarpusresearch.org We would like to thank A. DeVault at MycroArray for assistance optimizing the target enrichment protocol, and the Field Museum for use of its DNA sequencers. The authors thank B. Faircloth and two anonymous reviewers for helpful comments on an earlier version of the manuscript. This research was funded by National Science Foundation grants to A.J.S. (DEB‐1239980), B.G. (DEB‐1240045 and DEB‐1146295), N.J.W. (DEB‐1239992), and N.J.C.Z. (DEB‐0919119), and by a grant from the Northwestern University Institute for Sustainability and Energy (N.J.C.Z.). Data generated for this study can be found at ( and the NCBI Sequence Read Archive (SRA; BioProject PRJNA301299). , http://dx.doi.org/10.5061/dryad.3293r ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 We would like to thank A. DeVault at MycroArray for assistance optimizing the target enrichment protocol, and the Field Museum for use of its DNA sequencers. The authors thank B. Faircloth and two anonymous reviewers for helpful comments on an earlier version of the manuscript. This research was funded by National Science Foundation grants to A.J.S. (DEB-1239980), B.G. (DEB-1240045 and DEB-1146295), N.J.W. (DEB-1239992), and N.J.C.Z. (DEB-0919119), and by a grant from the Northwestern University Institute for Sustainability and Energy (N.J.C.Z.). Data generated for this study can be found at www.artocarpusresearch.org, www.datadryad.org (http://dx.doi.org/10.5061/dryad.3293r), and the NCBI Sequence Read Archive (SRA; BioProject PRJNA301299). |
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| Snippet | Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci,... Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high‐throughput sequence reads into loci,... Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of... Premise of the study:Using sequence data generated via target enrichment for phylogenetics requires reassembly of high‐throughput sequence reads into loci,... Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of highthroughput sequence reads into loci,... |
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| SubjectTerms | Artocarpus baits Bioinformatics computer software Deoxyribonucleic acid DNA exons Gene mapping Genes Genomes high-throughput nucleotide sequencing Hyb-Seq Introns loci Phylogenetics phylogenomics Phylogeny Plant sciences Scripts sequence assembly Software Note SOFTWARE NOTES |
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| Title | HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment |
| URI | http://www.bioone.org/doi/abs/10.3732/apps.1600016 https://onlinelibrary.wiley.com/doi/abs/10.3732%2Fapps.1600016 https://www.ncbi.nlm.nih.gov/pubmed/27437175 https://www.proquest.com/docview/2290713387 https://www.proquest.com/docview/1806075961 https://www.proquest.com/docview/2000177410 https://pubmed.ncbi.nlm.nih.gov/PMC4948903 |
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