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 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.

A Plastid Phylogeny of the Cosmopolitan Fern Family Cystopteridaceae (Polypodiopsida)

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The Parasitic Plant Genome Project: New Tools for Understanding the Biology ofOrobancheandStriga

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Using phylogenomics to resolve mega‐families: An example from Compositae

“…When obtaining fresh RNA (for phylogenomic approaches using transcriptome sequencing; e.g., Chan & Ragan, 2013) is not feasible as for museum or herbarium specimens, next-generation methods that make use of genomic DNA are necessary. Recent work in a number of taxonomic groups has utilized DNA sequence capture (target enrichment plus NGS) of conserved sequences for phylogenomic analyses (e.g., Faircloth et al, 2012;Mandel et al, 2014;Weitemier et al, 2014). Phylogenetic studies employing NGS have provided much insight into important evolutionary questions within these groups related to the timing and pattern of speciation events and elucidating relationships among key lineages (Liu et al, 2015).…”