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Transcriptome-mining for single-copy nuclear markers in ferns.

Carl J Rothfels1, Anders Larsson, Fay-Wei Li

  • 1Department of Biology, Duke University, Durham, North Carolina, United States of America ; Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.

Plos One
|October 12, 2013
PubMed
Summary
This summary is machine-generated.

Researchers developed 20 new nuclear markers for fern evolutionary studies, significantly expanding available resources. These markers offer improved phylogenetic resolution for the Polypodiales order and other fern groups.

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Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Genomics

Background:

  • Ferns are the second-most species-rich vascular plant group and sister to seed plants.
  • Previous fern phylogenetic studies heavily relied on plastid data due to a lack of nuclear genomic resources.
  • Nuclear and mitochondrial data have been underutilized in fern evolutionary research.

Purpose of the Study:

  • To design and validate novel nuclear markers for fern evolutionary biology.
  • To assess the utility of these markers across the Polypodiales, the largest fern order.
  • To provide resources for broader fern phylogenetic and evolutionary investigations.

Main Methods:

  • Utilized transcriptome data to design primers for 20 novel single-copy nuclear regions across 10 protein-coding genes.
  • Amplified and sequenced these markers from genomic DNA of 15 diploid Polypodiales species.
  • Developed transcriptome alignments for homologous loci across diverse fern taxa to facilitate primer design for non-Polypodiales species.

Main Results:

  • Successfully identified and presented 20 novel single-copy nuclear regions.
  • These regions demonstrated strong phylogenetic resolving power within the Polypodiales.
  • Phylogenetic analyses using these markers, partitioned by codon position, yielded a well-supported phylogeny consistent with previous studies.

Conclusions:

  • The 20 new nuclear regions more than triple the available single-copy nuclear markers for ferns.
  • These markers provide a crucial resource for testing plastid-derived phylogenetic hypotheses in ferns.
  • The study enhances the capacity to investigate previously inaccessible aspects of fern evolution.