Journal
APPLICATIONS IN PLANT SCIENCES
Volume 2, Issue 9, Pages -Publisher
WILEY
DOI: 10.3732/apps.1400042
Keywords
genome skimming; Hyb-Seq; nuclear loci; phylogenomics; species tree; target enrichment
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Funding
- U.S. National Science Foundation [DEB 0919583]
- Direct For Biological Sciences
- Division Of Environmental Biology [1311170, 0919389] Funding Source: National Science Foundation
- Direct For Biological Sciences
- Division Of Environmental Biology [0919583] Funding Source: National Science Foundation
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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.
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