Record Details
Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics
ScholarsArchive at Oregon State University
| Field | Value |
|---|---|
| Title | Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics |
| Names |
Weitemier, Kevin
(creator) Straub, Shannon C. K. (creator) Cronn, Richard C. (creator) Fishbein, Mark (creator) Schmickl, Roswitha (creator) McDonnell, Angela (creator) Liston, Aaron (creator) |
| Date Issued | 2014-07-01 (iso8601) |
| Note | 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. |
| 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 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. |
| Genre | Article |
| Topic | Genome skimming |
| Identifier | 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. |
