bioRxiv preprint doi: https://doi.org/10.1101/021246; this version posted June 19, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A targeted subgenomic approach for phylogenomics based on microfluidic PCR and high throughput sequencing Simon Uribe-Convers1,2,3,¶,*, Matthew L. Settles1,2,¶, David C. Tank1,2,3 1Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA 2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA 3Stillinger Herbarium, University of Idaho, Moscow, Idaho, USA *Corresponding author:
[email protected] (SUC) ¶These authors contributed equally to this work. bioRxiv preprint doi: https://doi.org/10.1101/021246; this version posted June 19, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses a Fluidigm microfluidic PCR array and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per microfluidic array).