Genomics / Proteomics
Douglas, Norman , Moore, Michael .
Using transcriptomic data to develop sequence-capture probes for diverse lineages.
Heretofore unprecedented amounts of data for phylogenetic and phylogeographic inference are theoretically available with the combination of sequence-capture techniques and hi-throughput, multiplexed Illumina sequencing. The application of this strategy hinges on the ability to design baits that will successfully capture genomic loci of interest. We have used available RNA-seq data, from lineages phylogenetically close to the taxa we wish to investigate (gypsophilic species of the Chihuahuan Desert), to design sequence capture baits by identifying transcripts homologous to 956 conserved orthologus sequences (COS loci). While conceptually simple, we found it necessary to use at least 13 programs and scripts to assemble the transcripts, identify homologous sequences, and prepare them for the bait design process. We discuss the rationales for the steps taken in this process, which should apply to anyone proposing to use transcriptomic data for phylogenetic and population genetic marker development. Finally, we present preliminary data on the performance of our methodology with respect to the number and percentage of loci covered, the success in obtaining variable intron data, and the effects of the phylogenetic distance between the target lineages and the species from which transcriptomic data were obtained.
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1 - Oberlin College, Department of Biology, 119 Woodland St., Oberlin, OH, 44074, USA
Presentation Type: Oral Paper:Papers for Topics
Location: Union B/Hyatt
Date: Wednesday, July 11th, 2012
Time: 10:45 AM