Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns
Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns Carl J. Rothfels1,2*, Anders Larsson3, Fay-Wei Li1, Erin M. Sigel1, Layne Huiet1, Dylan O. Burge4, Markus Ruhsam5, Sean W. Graham4, Dennis W. Stevenson6, Gane Ka-Shu Wong7,8, Petra Korall3, Kathleen M. Pryer1 1 Department of Biology, Duke University, Durham, North Carolina, United States of America, 2 Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada, 3 Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden, 4 Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada, 5 Royal Botanic Garden Edinburgh, Edinburgh, Scotland, 6 New York Botanical Garden, Bronx, New York, United States of America, 7 Department of Medicine, University of Alberta, Edmonton, Alberta, Canada, 8 BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China Abstract Background: Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns—the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. Principal Findings: We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin.
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