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Abstract Detail



Phylogenomics

Uribe-Convers, Simon [1], Duke, Justin R [1], Moore, Michael [2], Tank, David [1].

Got Genome? A long PCR based method for chloroplast genome enrichment and phylogenomics in angiosperms.

Premise of the study: We present a straightforward and cost-effective long PCR based method to amplify whole chloroplast genomes. Our method allows researchers to obtain large amounts of data from very small quantities of silica gel-dried or herbarium tissue (~0.02 g), as opposed to traditional plastome enrichment techniques that require large quantities of fresh tissue (~15 g). Methods and Results: We designed 58 universal chloroplast primer pairs that successfully amplify in three genera in Orobanchaceae and potentially across angiosperms. From these, 16 primer combinations were chosen to amplify the complete chloroplast genome in overlapping fragments that ranged from 5-12 kb. We sequenced these amplicons on an Illumina HiSeq, but they could be sequenced using any traditional or next-generation sequencing technology. Conclusions: We present a method to generate large amounts of genomic data from small quantities of tissue to provide an affordable, straightforward and efficient way to amplify complete chloroplast genomes.

Broader Impacts:


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Related Links:
Simon Uribe-Convers
Tank lab


1 - University of Idaho, College of Natural Resources & Institute for Bioinformatics and Evolutionary Studies, 875 Perimeter Drive MS 1133, Moscow, ID, 83844-1133
2 - Oberlin College, 119 Woodland St., Science Center K111, Oberlin, OH, 44074, USA

Keywords:
Angiosperms
chloroplast enrichment
chloroplast genome
long PCR
next generation sequencing.

Presentation Type: Oral Paper:Papers for Topics
Session: 36
Location: Magnolia/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 1:30 PM
Number: 36001
Abstract ID:325
Candidate for Awards:Margaret Menzel Award


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