Abstract Detail

Phylogenomics

Douglas, Norman [1], Leatherman, Lila [2], Mostow, Rebecca [1], Moore, Michael [3].

Phylogenomic analysis of Nyctaginaceae based on targeted enrichment of over 200 low-copy nuclear loci.

Targeted enrichment of nuclear loci has great potential to provide enormous amounts of sequence data for phylogenetic and population genetic studies. We first identified orthologs of known low-copy genes from transcriptome sequences from Boerhavia provided by the OneKP project. We then designed solution-based sequence capture baits targeted to 364 of these loci. These were used to enrich and sequence multiplexed paired-end genomic DNA libraries prepared for 35 taxa across 19 genera of Nyctaginaceae. Enriched libraries were then sequenced on both the MiSeq and HiSeq platforms. We report on the comparative success in enriching libraries at increasing phylogenetic distance from the species from which the baits were designed, the distribution of coverage within and between targeted loci, and the effectiveness in using exon-derived baits in enriching intron sequences. Our goals include analyses at multiple taxonomic levels, and thus we investigated the ability to phase alleles to haplotypes for phylogeographic analysis. Finally, we discuss new insights into the phylogeny of Nyctaginaceae based on these data.

Broader Impacts:

1 - Oberlin College, Department of Biology, 119 Woodland St, Oberlin, OH, 44074, USA
2 - Oberlin College, 119 Woodland St., Oberlin, Ohio, 44074, United States
3 - Oberlin College, 119 Woodland St., Science Center K111, Oberlin, OH, 44074, USA

Keywords:
Phylogenomics
Target Enrichment  
Sequence Capture
Nyctaginaceae.

Presentation Type: Oral Paper:Papers for Topics
Session: 36
Location: Magnolia/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 4:00 PM
Number: 36010
Abstract ID:758
Candidate for Awards:Margaret Menzel Award