rbcL and matK earn two thumbs up as the core DNA barcode for ferns.
Abstract
BACKGROUND: DNA barcoding will revolutionize our understanding of fern ecology, most
especially because the accurate identification of the independent but cryptic gametophyte
phase of the fern's life history--an endeavor previously impossible--will finally
be feasible. In this study, we assess the discriminatory power of the core plant DNA
barcode (rbcL and matK), as well as alternatively proposed fern barcodes (trnH-psbA
and trnL-F), across all major fern lineages. We also present plastid barcode data
for two genera in the hyperdiverse polypod clade--Deparia (Woodsiaceae) and the Cheilanthes
marginata group (currently being segregated as a new genus of Pteridaceae)--to further
evaluate the resolving power of these loci. PRINCIPAL FINDINGS: Our results clearly
demonstrate the value of matK data, previously unavailable in ferns because of difficulties
in amplification due to a major rearrangement of the plastid genome. With its high
sequence variation, matK complements rbcL to provide a two-locus barcode with strong
resolving power. With sequence variation comparable to matK, trnL-F appears to be
a suitable alternative barcode region in ferns, and perhaps should be added to the
core barcode region if universal primer development for matK fails. In contrast, trnH-psbA
shows dramatically reduced sequence variation for the majority of ferns. This is likely
due to the translocation of this segment of the plastid genome into the inverted repeat
regions, which are known to have a highly constrained substitution rate. CONCLUSIONS:
Our study provides the first endorsement of the two-locus barcode (rbcL+matK) in ferns,
and favors trnL-F over trnH-psbA as a potential back-up locus. Future work should
focus on gathering more fern matK sequence data to facilitate universal primer development.
Type
Journal articleSubject
FernsPteridaceae
Ribulose-Bisphosphate Carboxylase
Plant Proteins
Genetic Variation
Genetic Loci
DNA Barcoding, Taxonomic
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https://hdl.handle.net/10161/21735Published Version (Please cite this version)
10.1371/journal.pone.0026597Publication Info
Li, F; Kuo, L; Rothfels, CJ; Ebihara, A; Chiou, W; Windham, MD; & Pryer, KM (2011). rbcL and matK earn two thumbs up as the core DNA barcode for ferns. PloS one, 6(10). pp. e26597. 10.1371/journal.pone.0026597. Retrieved from https://hdl.handle.net/10161/21735.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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Kathleen M. Pryer
Professor of Biology

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