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

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https://ir.library.oregonstate.edu/concern/articles/sb397991j

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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 utilized to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq of twelve individuals (ten 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 nrDNA 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 datasets for phylogenomics.
  • This is an author's peer-reviewed final manuscript, as accepted by the publisher. The article is in press and will be published in Applications in Plant Sciences, Vol. 2, no. 9, September 2014.
  • Keywords: Genome skimming, Hyb-Seq, Target enrichment, Phylogenomics, Species tree, Nuclear loci
  • Keywords: Genome skimming, Hyb-Seq, Target enrichment, Phylogenomics, Species tree, Nuclear loci
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  • Weitemier, Kevin A., Shannon C. K. Straub, Richard C. Cronn, Mark Fishbein, Roswitha Schmickl, Angela McDonnell, Aaron Liston. 2014. Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics. Applications in Plant Sciences 2(9):1400042.
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  • 2
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  • 9
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  • This work was funded by the US National Science Foundation (DEB 0919583).
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