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Big data: A method for obtaining large, phylogenomic data sets
Date:1/9/2014

lowering plants. Surprisingly, the primers were even found to successfully amplify chloroplast regions in several pine species. To further test the compatibility of this approach with next-generation sequencing, 15 complete chloroplast genomes (often referred to as plastomes) were then sequenced.

Although this study focused on plastomes and utilized the popular Illumina sequencing platform, Uribe-Convers explains, "[t]his can easily be expanded to mitochondrial and nuclear regions, and can be used in combination with any next-generation sequencing platform. Furthermore, this approach is not restricted to plant studies, but will be useful for any organism."

With the development of new methods such as the one described by Uribe-Convers and colleagues, scientists can obtain large, phylogenomic data sets for large numbers of taxa. Long-range PCR, in concert with next-generation sequencing, provides researchers with the means to sequence entire plastomes, mitochondrial genomes, and large portions of the nuclear genome.

"This method has important implications for the way future systematic studies are conducted as it provides researchers with a way to strategically target regions of interest in their study organism, such as single-copy regions of the nuclear genome or portions of organellar genomes, to produce large data sets at low costs," says Uribe-Convers. "We want to help move the field of systematics into the realm of big data, and we hope that our approach contributes to that."


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Contact: Beth Parada
apps@botany.org
American Journal of Botany
Source:Eurekalert  

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