Abstract Detail

Genomics / Proteomics

Weitemier, Kevin [1], Straub, Shannon [1], Fishbein, Mark [2], Cronn, Richard [3], Liston, Aaron [1].

Genome-enabled phylogeography in Asclepias cryptoceras (Apocynaceae).

Molecular phylogeographic analyses using nuclear loci have traditionally required extensive preliminary work developing relatively small numbers of markers. High-throughput sequencing streamlines the development of genomic resources, offering orders of magnitude increases in potential nuclear markers. Draft genome and transcriptome assemblies produced as part of the Milkweed Genome Project for Asclepias syriaca (Apocynaceae), enabled development of markers suitable for targeted enrichment and hybridization capture (Hyb-Seq). Approximately 80,000 potentially single-copy and heterozygous single nucleotide polymorphisms (SNPs), associated with contigs greater than 1 kb, were identified in the A. syriaca genome assembly. To evaluate the utility of these markers in additional species, 4,000 candidate SNP loci were applied to a phylogeographic analysis of A. cryptoceras. This species is widely distributed across the Great Basin in western North America, and has two mostly disjunct varieties, with a small region of potential introgression. Over 800 loci comprised of 500-7744 bp of exonic sequence were also captured as part of a parallel phylogenetic study in Asclepias. This study will assess the utility of target capture in a species that is a congener of a model organism, and evaluate the advantages and disadvantages relative to high-throughput restriction based methods of population level analysis.

Broader Impacts:

Related Links:
Milkweed Genome Project

1 - Oregon State University, Department of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA
2 - Oklahoma State University, 301 Physical Sciences, Stillwater, OK, 74078, United States
3 - USDA Forest Service, 3200 SW Jefferson Way, Corvallis, OR, 97330, USA

Keywords:
Asclepias
Apocynaceae
Target Enrichment  
Hybridization sequencing
SNP
Next-generation sequencing
Phylogeography
Population genomics.

Presentation Type: Oral Paper:Papers for Topics
Session: 24
Location: Newberry/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 11:00 AM
Number: 24005
Abstract ID:775
Candidate for Awards:Margaret Menzel Award