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Abstract Detail

Genomics / Proteomics

Wenzel, Aaron [1], Blischak, Paul [2], Wolfe, Andrea [1].

Development of pentatricopetide repeat (PPR) markers for Penstemon using data from whole genome shotgun sequencing.

Despite their utility in plant systematics, low-copy nuclear genes are used less commonly than other loci because development of primers is time consuming and difficult. However, with the advent of the genomics revolution, it is becoming easier to discover nuclear loci. With tools such as whole genome shotgun sequencing and low coverage genome skimming, it is possible to identify nuclear genes of interest for marker development. One set of markers that has been shown to be useful in phylogenetic studies is the pentatricopeptide repeat (PPR) gene family. PPR proteins are comprised of 35-amino acid long repeats and have exhibited sufficient variation to resolve relationships at the genus and species levels. After discovering PPR sequences in whole genome shotgun sequence data for Penstemon, our goal was to develop primers for the available PPR sequences to be used in our phylogenetic analyses. After identification of PPR gene sequences, primers were designed for 14 loci using Primer-BLAST. All of the primers were screened via PCR-amplification on a subset of species representing two subgenera of Penstemon. Amplification was successful in all 14 loci; because some primer pairs produced multiple fragments, we selected only those that produced a single fragment, resulting in seven markers. Sequencing and analysis of these seven loci is currently in progress. We hope to further characterize this set of PPR markers and evaluate their usefulness in Penstemon.

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1 - Ohio State University, Department of Ecology, Evolution, And Organismal Biology, 318 W. 12th Avenue, COLUMBUS, OH, 43210-1293, USA
2 - Ohio State University, Evolution, Ecology & Organismal Biology, 318 W. 12th Avenue, Columbus, OH, 43210, USA

pentatricopeptide repeats
marker development
genome skimming.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Grand Salon A - D/Riverside Hilton
Date: Monday, July 29th, 2013
Time: 5:30 PM
Number: PGP008
Abstract ID:760
Candidate for Awards:None

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