Making next-generation sequencing work for you: approaches and practical considerations for marker development and phylogenetics

Recent reviews are setting the stage for the use of next-generation sequencing technologies in phylogenetic applications. However, the processes for developing new markers for phylogenetic analyses remain difficult to navigate for many researchers in plant systematics. We review several experimental approaches and practical considerations for developing new phylogenetic markers with next-generation sequencing technologies. We also outline a flexible framework for data acquisition that is readily adaptable to the needs of individual researchers and carefully consider cost-related issues that may be of concern to many laboratories in evolutionary biology. The next-generation and targeted sequencing approaches presented here offer considerable savings of time and money over the traditional PCR and Sanger sequencing approaches currently used in plant systematic research, particularly in cases involving large numbers of taxa and phylogenetic markers. Even with a limited research budget, next-generation sequence data can accommodate exploration of biological questions in ways that were not previously possible. Keywords: data miningmarker developmentnext-generation sequencingNGSorthologyphylogeneticsplant systematicsprimer developmenttargeted sequencing Acknowledgements The authors would like to thank the continued support and guidance of Pamela and Douglas Soltis, as well as their suggestions and edits during the development of this manuscript. In addition, we would like to thank Alex Twyford for his efforts in compiling this special feature and Brad Barbazuk, Nico Cellinese, Kenneth Jones, Steven Jordon, and Alan Prather for their helpful comments on the manuscript. Support for salaries is provided in part by NSF grant DEB-0919254 and a Fulbright-Conicyt (Chile) Doctoral Fellowship in Science and Technology. We also acknowledge the Herb Society of America for their support of next-generation research at the University of Florida. Notes †Authors contributed equally.