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•  Premise of the study:  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.  •  Methods and 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.

Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics