Journal
APPLICATIONS IN PLANT SCIENCES
Volume 5, Issue 3, Pages -Publisher
WILEY
DOI: 10.3732/apps.1600128
Keywords
Caryophyllales; cryogenic field sampling; phylogenomics; phylotranscriptomics; RNA
Categories
Funding
- University of Michigan
- Oberlin College
- National Geographic Society
- Chateaubriand Fellowship
- U.S. National Science Foundation [DGE 1144254, DEB 1054539, DEB 1352907, DEB 1354048]
- ERA-Net BiodivERsA project WhoIsNext
- national funders Agence Nationale de la Recherche (ANR) [ANR-13-EBID-0004]
- Deutsche Forschungsgemeinschaft (DFG)
- Fonds zur Forderung der wissenschaftlichen Forschung (FWF)
- Agence Nationale de la Recherche (ANR) [ANR-13-EBID-0004] Funding Source: Agence Nationale de la Recherche (ANR)
- Division Of Environmental Biology
- Direct For Biological Sciences [1352907] Funding Source: National Science Foundation
- NERC [NE/K009303/1] Funding Source: UKRI
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Premise of the study: We describe a field and laboratory workflow developed for plant phylotranscriptomic projects that involves cryogenic tissue collection in the field, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation. Methods and Results: A total of 216 frozen tissue samples of Caryophyllales and other angiosperm taxa were collected from the field or botanical gardens. RNA was extracted, stranded mRNA libraries were prepared, and libraries were sequenced on Illumina HiSeq platforms. These included difficult mucilaginous tissues such as those of Cactaceae and Droseraceae. Conclusions: Our workflow is not only cost effective (ca. $270 per sample, as of August 2016, from tissue to reads) and time efficient (less than 50 h for 10-12 samples including all laboratory work and sample curation), but also has proven robust for extraction of difficult samples such as tissues containing high levels of secondary compounds.
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