@ARTICLE{TreeBASE2Ref22302, author = {Carl J. Rothfels and Anders Larsson and Fay-Wei Li and Erin Mackey Sigel and Layne Huiet and Dylan Orion Burge and Markus Ruhsam and Sean W Graham and Dennis W. Stevenson and Gane Ka-Shu Wong and Petra Korall and Kathleen M. Pryer}, title = {Transcriptome-mining for Single-copy Nuclear Markers in Ferns}, year = {2013}, keywords = {ApPEFP_C; cryptochrome; DET1; fern phylogeny; gapCp; IBR3; model selection; partitioned analyses; pgiC; phylogenetics; Polypodiopsida; primer design; singlecopy nuclear markers; SQD1; TPLATE; transducin; transcriptomics}, doi = {}, url = {http://}, pmid = {}, journal = {PLoS ONE}, volume = {}, number = {}, pages = {}, abstract = {Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns?the second-most species-rich 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 novel 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. 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. These loci, both individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs?curated broadly across ferns?that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well supported and consistent with earlier studies of this group. The 20 novel single-copy regions presented here more than triple the single-copy nuclear regions available for use in fern phylogenetic inference. They provide a much needed opportunity to assess previous plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore many aspects of fern evolution previously unavailable to scientific investigation.} }

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