Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics

Abstract

• 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 confl ict between genomes. • Conclusions: The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and fl anking regions, as well as genome skimming of high-copy repeats and organellar genomes, to effi ciently produce genome-scale data sets for phylogenomics.

Citation

Weitemier, Kevin; Straub, Shannon C.K.; Cronn, Richard C.; Fishbein, Mark; Schmickl, Roswitha; McDonnell, Angela; Liston, Aaron. 2014. Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics. Applications in Plant Sciences. 2(9): Art. 1400042. 7 p.