Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?

Fazekas, Aron J.; Kesanakurti, Prasad; Burgess, Kevin S.; Percy, Diana M.; Graham, Sean W.; Barrett, Spencer C. H.; Newmaster, Steven G.; Hajibabaei, Mehrdad; Husband, Brian C.

doi:10.1111/j.1755-0998.2009.02652.x

Cited by 242 publications

(264 citation statements)

References 44 publications

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“…A threshold value calculated from genetic distances may be more appropriate than using a single arbitrary 1% or 3% threshold (Meier et al., 2006; Fazekas et al. 2009; Collins & Cruickshank, 2013). In this study, there was little change in the proportion of “correct,” “ambiguous,” and “incorrect” assignments when threshold values of 1%, 3% and a separate calculated threshold for each reference sequence library dataset were used.…”

Section: Discussionmentioning

confidence: 99%

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

Hosein

Austin

Maharaj

et al. 2017

Ecology and Evolution

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The islands of the Caribbean are considered to be a “biodiversity hotspot.” Collectively, a high level of endemism for several plant groups has been reported for this region. Biodiversity conservation should, in part, be informed by taxonomy, population status, and distribution of flora. One taxonomic impediment to species inventory and management is correct identification as conventional morphology‐based assessment is subject to several caveats. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species. In this study, the ability of DNA barcoding to confirm the identities of 14 endangered endemic vascular plant species in Trinidad was assessed using three DNA barcodes (matK, rbcL, and rpoC1). Herbarium identifications were previously made for all species under study. matK, rbcL, and rpoC1 markers were successful in amplifying target regions for seven of the 14 species. rpoC1 sequences required extensive editing and were unusable. rbcL primers resulted in cleanest reads, however, matK appeared to be superior to rbcL based on a number of parameters assessed including level of DNA polymorphism in the sequences, genetic distance, reference library coverage based on BLASTN statistics, direct sequence comparisons within “best match” and “best close match” criteria, and finally, degree of clustering with moderate to strong bootstrap support (>60%) in neighbor‐joining tree‐based comparisons. The performance of both markers seemed to be species‐specific based on the parameters examined. Overall, the Trinidad sequences were accurately identified to the genus level for all endemic plant species successfully amplified and sequenced using both matK and rbcL markers. DNA barcoding can contribute to taxonomic and biodiversity research and will complement efforts to select taxa for various molecular ecology and population genetics studies.

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Section: Discussionmentioning

confidence: 99%

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

Hosein

Austin

Maharaj

et al. 2017

Ecology and Evolution

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“…There is little doubt that the approaches used in plant DNA barcoding will be refined in future (22). However, the key foundation step for plant barcoding is in reaching agreement on a standard set of loci to enable large-scale sequencing and the development of a global plant barcoding infrastructure.…”

Section: Discussionmentioning

confidence: 99%

A DNA barcode for land plants

Hollingsworth¹,

Forrest²,

Spouge³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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2,125

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DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL؉matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.matK ͉ rbcL ͉ species identification L arge-scale standardized sequencing of the mitochondrial gene CO1 has made DNA barcoding an efficient species identification tool in many animal groups (1). In plants, however, low substitution rates of mitochondrial DNA have led to the search for alternative barcoding regions. From initial investigations of plastid regions (2-4), 7 leading candidates have emerged (5, 6). Four are portions of coding genes (matK, rbcL, rpoB, and rpoC1), and 3 are noncoding spacers (atpF-atpH, trnH-psbA, and psbK-psbI). Different research groups have proposed various combinations of these loci as their preferred plant barcodes, but no consensus has emerged (5-12). This lack of an agreed standard has impeded progress in plant barcoding.Our aim here is to identify a standard DNA barcode for land plants. To achieve this goal, we have pooled data across laboratories including sequence data from 907 samples, representing 445 angiosperm, 38 gymnosperm, and 67 cryptogam species. Using various subsets of these data, we evaluated the 7 candidate loci using criteria in the Consortium for the Barcode of Life's (CBOL) data standards and guidelines for locus selection (http:// www.barcoding.si.edu/protocols.html). Universality: Which loci can be routinely sequenced across the land plants? Sequence quality and coverage: Which loci are most amenable to the production of bidirectional sequences with few or no ambiguous base calls? Discrimination: Which loci enable most species to be distinguished? ResultsUniversality. Direct universality assessments using a single primer pair for each locus in angiosperms resulted in 90%-98% PCR and sequencing success for 6/7 regions. Success for the seventh region, psbK-psbI, was 77% (Fig. 1A). Greater problems were encountered in other land plant groups, with rpoB, matK, atpF-atpH, and psbK-psbI all showing Ͻ50% success in gymnosperms and/or cryptogams based on data compiled from several laboratories (Fig. 1 A).Sequence Quality. Evaluation of sequence quality and coverage from the candidate loci demonstrated that high quality bidirectional sequences were routinely obtained from rbcL, rpoC1, and rpoB (Fig. 1B, x axis). The remaining 4 loci required more manual editing and produced f...

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“…This study is one of the few that evaluated the efficacy of DNA barcoding among congeneric species (Salvia). Although our sampling was limited to a single genus, dense sampling within a genus and within species is necessary to clarify whether DNA barcoding can successfully delineate species rather than only higher taxonomic levels (e.g., to genus or species groups) (Fazekas et al, 2009;Pettengill and Neel, 2010). In conclusion, our study shows that ITS1 in the nuclear genome is the best DNA barcoding among the considered loci with sufficient variability and high identification efficiency (81.48%).…”

Section: Concluding Remarkmentioning

confidence: 74%

Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences

Wang

Zhao

Wang

et al. 2013

Gene

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Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?

Cited by 242 publications

References 44 publications

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

A DNA barcode for land plants

Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences

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