Choosing and Using a Plant DNA Barcode
PLoS ONEPublished 26 May 2011Open access
Peter M. Hollingsworth, Sean W. Graham, Damon P. Little
Citations1,308
SJR quartileQ1
SJR score0.80
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TL;DR
The process of selecting and refining a plant barcode is reviewed; the factors which influence the discriminatory power of the approach are evaluated; some early applications of plant barcoding are described and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcode to advance.
Abstract
The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.
Keywords
Biochemistry, Genetics and Molecular Biology
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An abundance of genomic information will have a broad range of applications, including not only helping conservation biologists understand ecosystem biodiversity, but also understanding the evolutionary histories of organisms, mending damaged landscapes, and investigating interactions of plants with pollinators and pests.
PLoS ONEParallel Loss of Plastid Introns and Their Maturase in the Genus Cuscuta
66 Citations2009Joel R. McNeal, Jennifer V. Kuehl +3 more
Examining matK and plastid intron distribution in Cuscuta adds support to the hypothesis that its normal role is in splicing seven of the eight group IIA introns in the genome, and analyzes matK nucleotide sequences from Cus cuta species and relatives that retain matK to test whether changes in selective pressure in the maturase are associated with intron deletion.
Annals of BotanyDNA barcoding: a new tool for palm taxonomists?
63 Citations2011Marc L. Jeanson, Jean‐Noël Labat +1 more
The results presented here are encouraging for developing DNA barcoding as a useful tool to identify species within this ecologically important tropical plant family.
Anales del Jardín Botánico de MadridUniversal primers for the amplification of the plastid trnK/matK region in land plants
63 Citations2009Susann Wicke, Dietmar Quandt
Cebadores universales para the amplificacion of the plastid trnK/matK region in land plants in plantas te rrestres are presented.
TaxonA stuttering start to plant DNA barcoding: microsatellites present a previously overlooked problem in non‐coding plastid regions
62 Citations2009Dion S. Devey, Mark W. Chase +1 more
This paper investigates the suitability of the psbA-trnH and atpF-H regions of the plastid genome for automated barcoding purposes and shows evidence of microsatellite-induced errors in electropherogram base calling.
Molecular Ecology ResourcesDNA barcoding discriminates the noxious invasive plant species, floating pennywort (<i>Hydrocotyle ranunculoides</i> L.f.), from non‐invasive relatives
56 Citations2009C.C.M. van de Wiel, J. van der Schoot +3 more
It is shown that it is possible to distinguish H. ranunculoides from a series of closely related congeners by using a single plastid DNA sequence, trnH‐psbA.
Plant Systematics and EvolutionIdentifying a mysterious aquatic fern gametophyte
56 Citations2009Fay‐Wei Li, Benito C. Tan +5 more
The phylogenetic analyses showed that Süßwassertang is nested within the hemi-epiphytic fern genus Lomariopsis (Lomariopsidaceae) and aligned very close to L. lineata, and it is of great interest to discover that a fern usually known to grow on trees also has gametophytes that thrive in water.
Molecular and General Genetics MGGDuplication of the psbA gene in the chloroplast genome of two Pinus species
52 Citations1991Jonas Lidholm, Alfred E. Szmidt +1 more
The psbA gene, encoding the D1 protein of photosystem II, was found to be duplicated in the chloroplast genome of two pine species, Pinus contorta and P. banksiana, and analysis of cloned overlapping restriction fragments showed that the two PsbA genes have the same orientation and are separated by approximately 3.3 kb.
EvolutionPHYLOGEOGRAPHIC PATTERNS AND HIGH LEVELS OF CHLOROPLAST DNA DIVERSITY IN FOUR PACKERA (ASTERACEAE) SPECIES IN SOUTHWESTERN ALBERTA
51 Citations2000Joanne L. Golden, John F. Bain
It is proposed that Pleistocene hybridization and incomplete lineage sorting have resulted in reduced subdivision of interpopulational variation so that gene flow may not be as high as indicated.
Systematic BiologyMapping Uncertainty and Phylogenetic Uncertainty in Ancestral Character State Reconstruction: An Example in the Moss Genus Brachytheciastrum
51 Citations2006Alain Vanderpoorten, Bernard Goffinet
The Bayesian approach of ancestral character state reconstruction offers a series of advantages over the single-tree approach or the ML model optimization on a Bayesian sample of trees because it does not involve restricting model parameters prior to reconstructing ancestral states, but rather allows a range of model parameters and ancestral character states to be sampled according to their posterior probabilities.
Molecular Ecology ResourcesPotential DNA transfer from the chloroplast to the nucleus in <i>Eryngium alpinum</i>
46 Citations2009Yamama Naciri, Jean-François Manen
Quantitative polymerase chain reactions confirmed the hypothesis that very divergent psbA‐trnH chloroplast sequences are paraloguous fragments transferred into the nucleus (NuPt), which might have severe implications in plant phylogeography and barcoding.
BMC Evolutionary BiologyUnveiling cryptic species diversity of flowering plants: successful biological species identification of Asian Mitella using nuclear ribosomal DNA sequences
44 Citations2009Yudai Okuyama, Makoto Katô
It is proposed that nuclear ribosomal DNA sequences contribute to reliable identification of reproductively isolated and cryptic species of Mitella.
Molecular Ecology NotesIdentifying fern gametophytes using DNA sequences
43 Citations2006Harald Schneider, Eric Schuettpelz
It is evident that DNA-based identification has considerable potential in exploring the ecology of fern gametophytes, and the usefulness of rbcL in differentiating among species is evaluated.
TaxonDNA barcoding of African Podostemaceae (river‐weeds): A test of proposed barcode regions
40 Citations2010Laura J. Kelly, Gabriel Ameka +1 more
The results show that although the rpoCl region performs best in terms of universality of amplification and sequencing, the superior resolving power of matK makes it the most promising of the regions for use in barcoding.
Current GeneticsThe chloroplast genome of the gymnosperm Pinus contorta: a physical map and a complete collection of overlapping clones
39 Citations1991Jonas Lidholm, Petter Gustafsson
Overlapping restriction fragments of chloroplast DNA from the conifer Pinus contorta were cloned and the genome appeared essentially colinear with that of Pinus radiata, for which a map has previously been published.
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