title: Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics.
abstract: OBJECTIVE
  Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. •
  
  
  RESULTS
  Genome and transcriptome assemblies for milkweed (Asclepias syriaca) were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera) resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. •
  
  
  CONCLUSIONS
  The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331 USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Weitemier
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331 USA.
authors.forename: Shannon C K
authors.initials: SC
authors.lastname: Straub
authors.affiliation: Pacific Northwest Research Station, USDA Forest Service, 3200 SW Jefferson Way, Corvallis, Oregon 97331 USA.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Cronn
authors.affiliation: Department of Botany, Oklahoma State University, 301 Physical Sciences, Stillwater, Oklahoma 74078 USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Fishbein
authors.affiliation: Institute of Botany, Academy of Sciences of the Czech Republic, CZ-25243 Průhonice, Czech Republic.
authors.forename: Roswitha
authors.initials: R
authors.lastname: Schmickl
authors.affiliation: Department of Botany, Oklahoma State University, 301 Physical Sciences, Stillwater, Oklahoma 74078 USA.
authors.forename: Angela
authors.initials: A
authors.lastname: McDonnell
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331 USA.
authors.forename: Aaron
authors.initials: A
authors.lastname: Liston
keywords: Hyb-Seq; genome skimming; nuclear loci; phylogenomics; species tree; target enrichment