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Abstract Detail


Wills, Peter [1], Gernandt, David S. [2], Vasquez Lobo, Alejandra [3], Willyard, Ann [4].

Phylogenomics of the Ponderosa Pine Species Complex using High Throughput Sequencing.

Species-level phylogenetics using plastid genes or just a few nuclear genes has proven ineffective at resolving groups like the ponderosa pine species complex where incomplete lineage sorting and plastid transfers create conflicting species trees depending on the data used. High throughput sequencing provides a cost-effective method of sequencing the hundreds of genes needed to resolve some species trees. Enrichment of targeted low-copy nuclear loci via biotinylated RNA probes reduces the complexity of plant genomes, producing much more useful data for the determination of these genetic relationships. The goal of the experiment was to sequence at least 100 low-copy nuclear genes from each putative species. We designed our probes for 700 low-copy nuclear loci from a list of published pine sequences. Sheared DNA was hybridized in solution to the biotinylated probes to enrich for these low-copy loci and their flanking regions prior to Illumina sequencing with 100 bp paired end reads. We used genomic skimming to assemble plastome, high-copy nuclear ribosomal, and mitochondrial sequences, and de novo and reference-guided assembly to arrange the raw reads, and filter out putative paralogs using multi-sequence alignments. We investigated the feasibility of aligning introns and non-coding regions of the genome that we obtained along with the targeted exons, which we expected to provide additional means of determining low order taxonomic relations among pine populations. We selected a group of the most reliably aligned genes to create gene trees, which were in turn used to build a species tree.

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1 - Hendrix College, Biology Department, 1600 Washington Ave, Conway, AR, 72032, USA
2 - Instituto De Biologia, UNAM, Apartado Postal 70-233, Coyoacan, Mexico, N/A, 04510, Mexico
3 - Universidad Autonoma del Estado de Morelos, Centro de Investigacion en Biodiversidad y Conservacion, Universidad No. 1001, Cuernavaca, Morelos, 62209, Mexico
4 - Hendrix College, Biology Dept, 1600 Washington Ave, Conway, AR, 72032, USA

low-copy nuclear markers
species tree

Presentation Type: Poster
Session: P, Phylogenomics Posters
Location: Exhibit Hall/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 5:30 PM This poster will be presented at 5:30 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PPY005
Abstract ID:306
Candidate for Awards:None

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