HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

Matthew G. Johnson; Elliot M. Gardner; Yang Liu; Rafael Medina; Bernard Goffinet; A. Jonathan Shaw; Nyree J.C. Zerega; Norman J. Wickett

doi:10.3732/apps.1600016

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

Matthew G. Johnson^*, Elliot M. Gardner, Yang Liu, Rafael Medina, Bernard Goffinet, A. Jonathan Shaw, Nyree J.C. Zerega, Norman J. Wickett

^*Corresponding author for this work

Program in Biological Sciences

Research output: Contribution to journal › Article › peer-review

413 Scopus citations

Abstract

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 OSX and is freely available at https://github.com/mossmatters/HybPiper.

Original language	English (US)
Article number	1600016
Journal	Applications in Plant Sciences
Volume	4
Issue number	7
DOIs	https://doi.org/10.3732/apps.1600016
State	Published - Jul 1 2016

Keywords

Hyb-Seq
bioinformatics
phylogenomics
sequence assembly

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Plant Science

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10.3732/apps.1600016

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title = "HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment",

abstract = "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 OSX and is freely available at https://github.com/mossmatters/HybPiper.",

keywords = "Hyb-Seq, bioinformatics, phylogenomics, sequence assembly",

author = "Johnson, {Matthew G.} and Gardner, {Elliot M.} and Yang Liu and Rafael Medina and Bernard Goffinet and Shaw, {A. Jonathan} and Zerega, {Nyree J.C.} and Wickett, {Norman J.}",

note = "Funding Information: 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.). Publisher Copyright: {\textcopyright} 2016 Johnson et al. Published by the Botanical Society of America.",

year = "2016",

month = jul,

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doi = "10.3732/apps.1600016",

language = "English (US)",

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T2 - Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

AU - Johnson, Matthew G.

AU - Gardner, Elliot M.

AU - Liu, Yang

AU - Medina, Rafael

AU - Goffinet, Bernard

AU - Shaw, A. Jonathan

AU - Zerega, Nyree J.C.

AU - Wickett, Norman J.

N1 - Funding Information: 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.). Publisher Copyright: © 2016 Johnson et al. Published by the Botanical Society of America.

PY - 2016/7/1

Y1 - 2016/7/1

N2 - 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 OSX and is freely available at https://github.com/mossmatters/HybPiper.

AB - 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 OSX and is freely available at https://github.com/mossmatters/HybPiper.

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KW - bioinformatics

KW - phylogenomics

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HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

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