Journal
PLANT ECOLOGY & DIVERSITY
Volume 5, Issue 4, Pages 427-450Publisher
TAYLOR & FRANCIS LTD
DOI: 10.1080/17550874.2012.745909
Keywords
data mining; marker development; next-generation sequencing; NGS; orthology; phylogenetics; plant systematics; primer development; targeted sequencing
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Funding
- NSF [DEB-0919254]
- Fulbright-Conicyt (Chile) Doctoral Fellowship in Science and Technology
- Herb Society of America
- Direct For Biological Sciences
- Division Of Environmental Biology [1210671] Funding Source: National Science Foundation
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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.
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