Molecular Ecology and Evolution
Heyduk, Karolina , Trapnell, Dorset , Leebens-Mack, Jim .
A gene capture approach for determining species relationships within Sabal.
With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer limited by the use of a few loci. Using available transcriptome data for the genus Sabal, a palm in the Corypheae tribe, and sequence data from 4 other genera within the Arecaceae, we designed probes for the selective capture of genic regions in the palm genomes. Sequences from Sabal were aligned with orthologs from the genera Elaeis, Phoenix, Nypa, and Cocos and were selected for gene capture based on BLAST hits to a low-copy set of angiosperm gene families. Genes were further filtered by pairwise distance measures among orthologous genes sorted to a low-copy gene family. The longest sequence in each low-copy gene family alignment was chosen as the exemplar used to determine intron-exon boundaries. Exon sequences were identified from 176 gene family exemplars, with an average of 4.76 exons per gene. By selecting for low copy sequences that are highly conserved, we can capture genomic regions for targeted high-throughput sequencing across the Arecaceae. Our initial investigation focuses on the genus Sabal and the origin of the island endemic, Sabal bermudana. Beyond Sabal, we will test the utility of the probe set for phylogenetic analysis across the Arecaceae.
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1 - University of Georgia, Plant Biology, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
2 - University Of Georgia, Department Of Plant Biology, 2502 Miller Plant Sciences Building, Athens, GA, 30602, USA
3 - University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
Presentation Type: Poster:Posters for Topics
Location: Battelle South/Convention Center
Date: Monday, July 9th, 2012
Time: 5:30 PM