G. Johnson, MatthewGardner, Elliot M.Liu, YangMedina Bujalance, RafaelGoffinet, BernardShaw, A. JonathanZerega, Nyree J. C.Wickett, Norman J.2024-01-262024-01-262016-07-012168-04502168-045010.3732/apps.1600016https://hdl.handle.net/20.500.14352/95646This 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).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.engjournal articlehttps://bioone.org/journals/applications-in-plant-sciences/volume-4/issue-7/apps.1600016/HybPiper--Extracting-Coding-Sequence-and-Introns-for-Phylogenetics-from/10.3732/apps.1600016.fullhttp://dx.doi.org/10.5061/dryad.3293ropen access181.15bioinformatics; Hyb-Seq; phylogenomics; sequence assembly.Biología molecular (Biología)2415.02 Biología Molecular de Plantas