Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective

Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK) is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes--while playing an ess...

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Bibliographic Details
Published in:PloS one 2011-01, Vol.6 (1), p.e16371-e16371
Main Authors: de Groot, G Arjen, During, Heinjo J, Maas, Jan W, Schneider, Harald, Vogel, Johannes C, Erkens, Roy H J
Format: Article
Language:English
Subjects:
amplification
Analysis
Asplenium
Bar codes
Biodiversity
Biology
chloroplast dna
Chloroplasts
Colonization
Deoxyribonucleic acid
DNA
DNA Barcoding, Taxonomic
Dryopteridaceae
Dryopteris
Dryopteris carthusiana
Dryopteris cristata
dryopteris-affinis group
Ecological monitoring
Ecological studies
Ecology
Ecosystem
Europe
Ferns
Ferns - classification
Ferns - genetics
Gametophytes
Gene sequencing
Genetic diversity
Genetic Markers
Genomes
Genomics
Identification
Interspecific
land plants
Loci
Markers
mononucleotide repeats
Morphology
Multiculturalism & pluralism
Museums
noncoding regions
pcr
phylogeny
Plant sciences
Plastids
Polyploidy
Primers
Ribulose-Bisphosphate Carboxylase - genetics
sequences
Species
Taxa
taxonomy
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Summary:Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK) is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes--while playing an essential role in fern colonization and reproduction--generally lack the morphological complexity for morphology-based identification and have therefore been underappreciated in ecological studies. We evaluated the potential of a combination of rbcL with a noncoding plastid marker, trnL-F, to obtain DNA-identifications for fern species. A regional approach was adopted, by creating a reference database of trusted rbcL and trnL-F sequences for the wild-occurring homosporous ferns of NW-Europe. A combination of parsimony analyses and distance-based analyses was performed to evaluate the discriminatory power of the two-region barcode. DNA was successfully extracted from 86 tiny fern gametophytes and was used as a test case for the performance of DNA-based identification. Primer universality proved high for both markers. Based on the combined rbcL + trnL-F dataset, all genera as well as all species with non-equal chloroplast genomes formed their own well supported monophyletic clade, indicating a high discriminatory power. Interspecific distances were larger than intraspecific distances for all tested taxa. Identification tests on gametophytes showed a comparable result. All test samples could be identified to genus level, species identification was well possible unless they belonged to a pair of Dryopteris species with completely identical chloroplast genomes. Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species. A regional approach may be preferred for ecological tests. We here offer such a ready-to-use barcoding approach for ferns, which opens the way for answering a whole range of questions previously unaddressed in fern gametophyte ecology.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0016371