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Abstract Detail



Phylogenomics

Mast, Austin [1], Buddenhagen, Christopher [1], Lemmon, Alan R. [2].

Anchored Phylogenomics in the Angiosperms.

Individual gene trees can differ significantly from species trees due to such processes as coalescence stochasticity, hybridization/introgression, and polyploidization. Targeted enrichment of DNA libraries prior to next generation sequencing permits the assembly of datasets with 100s or 1000s of putatively orthologous loci from across the genome for more robust species tree inference. New methods of this type have relied on variability of regions flanking either ultraconserved elements (with 100% similarity) or relatively conserved (at least 65% similar) stretches of the genome in animals as sources of phylogenetic data. Since ultraconserved elements are fewer and mainly non-syntenic in plants (suggesting that they might not share a long evolutionary history with their flanking regions), we adopt the more relaxed selection criterion. Using genome alignments from model organisms and our own low-coverage (20X) genome sequencing from a strategic sampling of non-model organisms, we identified 1000s of potentially useful probe target sites in angiosperms. We will present an overview of the bioinformatics pipeline for identifying the probe target sites, the distribution of these target sites in the genome of a model plant, and an assessment of variability of regions bordering the target sites (in the context of utility for resolving deep vs. shallow cladogenetic events). This is a first step in the potentially transformative goal of producing a targeted sequence enrichment kit for angiosperms that facilitates future phylogenomics (by removing the marker development step) and maximizes data combinability across studies. If time permits, we will also present the first application of this target enrichment kit in a group of closely related monocots (the beaksedges; Rhynchospora, Cyperaceae).

Broader Impacts:


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1 - Florida State University, Department of Biological Science, 319 Stadium Drive, Tallahassee, FL, 32306, USA
2 - Florida State University, Department of Scientific Computing, 150-A Dirac Science Library, Tallahassee, FL, 32306-4120, USA

Keywords:
Angiosperms
Anchored Enrichment
Anchored Phylogenomics
Cyperaceae
Monocots
Phylogenomics
phylogeny
Rhynchospora
Sequence Capture
Target Enrichment.

Presentation Type: Oral Paper:Papers for Topics
Session: 36
Location: Magnolia/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 1:45 PM
Number: 36002
Abstract ID:539
Candidate for Awards:None


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