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Citation for Study 14616

Citation title: "Transcriptome-mining for Single-copy Nuclear Markers in Ferns".

Study name: "Transcriptome-mining for Single-copy Nuclear Markers in Ferns".

This study is part of submission 14616 (Status: Published).

Citation

Rothfels C., Larsson A., Li F., Sigel E.M., Huiet L., Burge D.O., Ruhsam M., Graham S.W., Stevenson D., Wong G.K., Korall P., & Pryer K. 2013. Transcriptome-mining for Single-copy Nuclear Markers in Ferns. PLoS ONE, .

Authors

• Rothfels C.
• Larsson A.
• Li F.
• Sigel E.M. (802) 578-7146
• Huiet L.
• Burge D.O. 9194336011
• Ruhsam M.
• Graham S.W.
• Stevenson D.
• Wong G.K.
• Korall P.
• Pryer K.

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.

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

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S14616
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@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.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 22302
  AU  - Rothfels,Carl J. 
  AU  - Larsson,Anders 
  AU  - Li,Fay-Wei 
  AU  - Sigel,Erin  Mackey
  AU  - Huiet,Layne 
  AU  - Burge,Dylan Orion
  AU  - Ruhsam,Markus 
  AU  - Graham,Sean W
  AU  - Stevenson,Dennis W. 
  AU  - Wong,Gane Ka-Shu 
  AU  - Korall,Petra 
  AU  - Pryer,Kathleen M. 
  T1  - Transcriptome-mining for Single-copy Nuclear Markers in Ferns
  PY  - 2013
  KW  - ApPEFP_C; cryptochrome; DET1; fern phylogeny; gapCp; IBR3; model selection; partitioned analyses; pgiC; phylogenetics; Polypodiopsida; primer design; singlecopy nuclear markers; SQD1; TPLATE; transducin; transcriptomics
  UR  - http://dx.doi.org/
  N2  - 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.
  L3  - 
  JF  - PLoS ONE
  VL  - 
  IS  - 
  ER  -