A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

Kress, W. John; Erickson, David L.

doi:10.1371/journal.pone.0000508

Cited by 1,251 publications

(1,356 citation statements)

References 34 publications

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“…2011). Others have reported low resolution in rbcL because it is known to have insufficient nucleotide sequence variability to distinguish among closely related species (Kress & Erickson, 2007; Newmaster, Grguric, Shanmughanandhan, Ramalingam, & Ragupathy, 2013). …”

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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“…Three parameters were used to compare intraspecific divergence (Lahaye et al, 2008;Meyer and Paulay, 2005): (i) the mean of all intraspecific distances within species with at least two individuals; (ii) the "mean theta," where theta is the average pairwise distance calculated within species to eliminate biases associated with different samplings among species; and (iii) the average coalescent depth, that is, the maximum distance within each species. Wilcoxon signed-rank tests were performed to compare intraspecific variability and the interspecific variability of every pair of barcodes following Kress and Erickson (2007). The barcoding gaps were evaluated by comparing the distribution of interspecific/intraspecific divergence.…”

Section: Resultsmentioning

confidence: 99%

“…However, the NJ tree indicated that the species with different higher-level phylogenies, such as the subgenus and the genus (the outgroup), can be distinguished. Numerous other studies also suggested that rbcL is only suitable for DNA barcode at the genus level (and above) (Kress and Erickson, 2007;Newmaster et al, 2006;Sass et al, 2007).…”

Section: Applicability Of the Candidate Chloroplast Dna Barcodesmentioning

confidence: 99%

“…It has a short average length, mostly approximately 450 bp, which is conducive for amplifying degradable material (Shaw et al, 2005). Based on these characteristics, it was identified as a highly accurate potential candidate marker (Kress and Erickson, 2007;Kress et al, 2005). Although psbA-trnH has highly variable interspecific distances for Salvia, it also has the highest intraspecific distances.…”

Section: Applicability Of the Candidate Chloroplast Dna Barcodesmentioning

confidence: 99%

“…Compared with the barcodes in the chloroplast, ITS showed a high interspecific variation and discriminatory power, accurately discriminating 70.37% of all species tested. Kress and Erickson (2007) pointed out that ITS has multiple copies in the nuclear genome and it varies within species, which limits its application. In contrast to Salvia, most of these copies were diploids Yang et al, 2009).…”

Section: Applicability Of Nritsmentioning

confidence: 99%

See 2 more Smart Citations

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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Identification of Medicinal Plants UsingDNABarcoding Technique

Pang

Chen

2014

Encyclopedia of Analytical Chemistry

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The accurate identification of medicinal plants in relation to their purity and quality as well as safe application has become increasingly important. DNA barcoding is an established technique that uses the sequence diversity in short, standard DNA regions for species‐level identification. It is primarily used to identify known species by comparing their unique barcode sequences to reference sequences in public databases, as well as to facilitate species discovery. DNA barcoding provides a more rapid, subjective, and accurate identification compared with traditional methods. Thus, it has rapidly become a widely recognized tool for species identification. Chen et al . provided a comprehensive evaluation of different DNA regions for the authentication of medicinal plants. They found that the second internal transcriber spacer (ITS2) region could be used as a universal barcode for plant authentication. The ITS2 barcode has been tested recently in a wide range of taxa. It has been proven to be effective for identifying medicinal plants. In this study, we introduce the DNA barcoding technique and determine its usage in discriminating medicinal plants, as well as its advantages and limitations.

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A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

Cited by 1,251 publications

References 34 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

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

Identification of Medicinal Plants UsingDNABarcoding Technique

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