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Transcriptome-mining for single-copy nuclear markers in ferns.
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. These loci, 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. CONCLUSIONS:The
20 single-copy regions presented here more than triple the single-copy nuclear regions
available for use in ferns. They provide a much-needed opportunity to assess plastid-derived
hypotheses of relationships within the ferns, and increase our capacity to explore
aspects of fern evolution previously unavailable to scientific investigation.
Type
Journal articleSubject
Cell NucleusFerns
Plant Proteins
Gene Expression Profiling
Sequence Analysis, DNA
Evolution, Molecular
Phylogeny
Gene Expression Regulation, Plant
Gene Dosage
Genes, Plant
Molecular Sequence Data
Transcriptome
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https://hdl.handle.net/10161/21734Published Version (Please cite this version)
10.1371/journal.pone.0076957Publication Info
Rothfels, CJ; Larsson, A; Li, F; Sigel, EM; Huiet, L; Burge, DO; ... Wong, GK (2013). Transcriptome-mining for single-copy nuclear markers in ferns. PloS one, 8(10). pp. e76957. 10.1371/journal.pone.0076957. Retrieved from https://hdl.handle.net/10161/21734.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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