Choosing and Using a Plant DNA Barcode
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.
Citations
More filters
TL;DR: GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping and are able to reassemble the circular Plastomes from 47 datasets using GetOrganelle.
Abstract: GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (
https://github.com/Kinggerm/GetOrganelle
).
1,160 citations
TL;DR: It is proposed that ITS/ITS2 should be incorporated into the core barcode for seed plants, because in cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplified and sequence this subset of the marker.
Abstract: A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.
711 citations
TL;DR: A new approach is advocate that, for selected groups of taxa, combines the best use of single‐locus barcodes and super‐barcodes for efficient plant identification, and discusses the feasibility of using the chloroplast genome as a super-barcode.
Abstract: DNA barcoding is currently a widely used and effective tool that enables rapid and accurate identification of plant species; however, none of the available loci work across all species Because single-locus DNA barcodes lack adequate variations in closely related taxa, recent barcoding studies have placed high emphasis on the use of whole-chloroplast genome sequences which are now more readily available as a consequence of improving sequencing technologies While chloroplast genome sequencing can already deliver a reliable barcode for accurate plant identification it is not yet resource-effective and does not yet offer the speed of analysis provided by single-locus barcodes to unspecialized laboratory facilities Here, we review the development of candidate barcodes and discuss the feasibility of using the chloroplast genome as a super-barcode We advocate a new approach for DNA barcoding that, for selected groups of taxa, combines the best use of single-locus barcodes and super-barcodes for efficient plant identification Specific barcodes might enhance our ability to distinguish closely related plants at the species and population levels
536 citations
Cites background from "Choosing and Using a Plant DNA Barc..."
...Hollingsworth, Graham & Little (2011) argued that the full plastid haplotype is not a good marker because it does not always track species boundaries....
[...]
TL;DR: Chloroplast genome sequences contain regions that are highly variable, and these regions are the first consideration when screening the suitable loci to resolve closely related species or genera in phylogenetic analyses, and for DNA barcoding.
Abstract: Background
At present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species
496 citations
Cites background from "Choosing and Using a Plant DNA Barc..."
...Some regions of the chloroplast genome, for example, atpF-H, matK, psbK-I, rbcL, rpoB, rpoC1 and trnH-psbA have been relied upon heavily for development of candidate markers for plant DNA barcoding [8,9,10,11,12]....
[...]
TL;DR: Most of the herbal products tested were of poor quality, including considerable product substitution, contamination and use of fillers, which suggests that the herbal industry should embrace DNA barcoding for authenticating herbal products through testing of raw materials used in manufacturing products.
Abstract: Background: Herbal products available to consumers in the marketplace may be contaminated or substituted with alternative plant species and fillers that are not listed on the labels According to the World Health Organization, the adulteration of herbal products is a threat to consumer safety Our research aimed to investigate herbal product integrity and authenticity with the goal of protecting consumers from health risks associated with product substitution and contamination Methods: We used DNA barcoding to conduct a blind test of the authenticity for (i) 44 herbal products representing 12 companies and 30 different species of herbs, and (ii) 50 leaf samples collected from 42 herbal species Our laboratory also assembled the first standard reference material (SRM) herbal barcode library from 100 herbal species of known provenance that were used to identify the unknown herbal products and leaf samples Results: We recovered DNA barcodes from most herbal products (91%) and all leaf samples (100%), with 95% species resolution using a tiered approach (rbcL + ITS2) Most (59%) of the products tested contained DNA barcodes from plant species not listed on the labels Although we were able to authenticate almost half (48%) of the products, one-third of these also contained contaminants and or fillers not listed on the label Product substitution occurred in 30/44 of the products tested and only 2/12 companies had products without any substitution, contamination or fillers Some of the contaminants we found pose serious health risks to consumers Conclusions: Most of the herbal products tested were of poor quality, including considerable product substitution, contamination and use of fillers These activities dilute the effectiveness of otherwise useful remedies, lowering the perceived value of all related products because of a lack of consumer confidence in them We suggest that the herbal industry should embrace DNA barcoding for authenticating herbal products through testing of raw materials used in manufacturing products The use of an SRM DNA herbal barcode library for testing bulk materials could provide a method for ‘best practices’ in the manufacturing of herbal products This would provide consumers with safe, high quality herbal products Background Globalization of trade is expanding natural product commodity markets that sustain life and promote good health, yet the challenging financial climate is squeezing profit margins and exacerbating the propensity for contamination, fraudulent market substitution and the use of unlabeled fillers This comes at a time when consumers are becoming increasingly concerned about the authenticity of the products they purchase North America is a major provider of goods such as herbal products, a commodity that has come under scrutiny recently in the media due to product substitution [1-3] The International Trade in herbal products is a major force in the global economy and the demand is increasing in both developing and developed nations There are currently more than 1,000 companies producing medicinal plant products with annual revenues in excess of US$60 billion Notably, medicinal herbs now constitute the most rapidly growing segment of the North American alternative medicine market [4,5], with over 29,000 herbal substances [6,7] generating billions of dollars in trade These statistics are indicative of the rapid growth
427 citations
Cites result from "Choosing and Using a Plant DNA Barc..."
...Other published studies have also encountered similar problems [47-51]....
[...]
References
More filters
TL;DR: It is established that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals and will provide a reliable, cost–effective and accessible solution to the current problem of species identification.
Abstract: Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
9,879 citations
TL;DR: Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed and worked for most species tested, which means that they may be used to study the population biology and evolution of plants.
Abstract: Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
5,212 citations
"Choosing and Using a Plant DNA Barc..." refers background in this paper
...This frequent use is attributable to the early publication of a robust set of primers that allow routine recovery [41]....
[...]
3,792 citations
29 Aug 2012
TL;DR: It was established previously that the mitochondrial gene cytochrome c oxidase I can serve as the core of a global bioidentification system for animals and a new tools were developed recently to be complementary markers for (COI) DNA barcoding.
Abstract: Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon ‘barcodes’. It was established previously that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. A new tools were developed recently to be complementary markers for (COI) DNA barcoding.
2,945 citations
"Choosing and Using a Plant DNA Barc..." refers background in this paper
...The standard animal CO1 DNA barcode fits these criteria well [1]....
[...]
Royal Botanic Garden Edinburgh1, National Institutes of Health2, University of Guelph3, University of Johannesburg4, Royal Botanic Gardens5, Smithsonian Institution6, University of British Columbia7, Natural History Museum8, Korea University9, University of Toronto10, State University of Feira de Santana11, University of Costa Rica12, Columbus State University13, New York Botanical Garden14, University of Wisconsin-Madison15, University of the Andes16, University of Cape Town17, Seoul National University18, Hallym University19, National Autonomous University of Mexico20, Imperial College London21
TL;DR: The 2-locus combination of rbcL+matK 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.
Abstract: 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.
2,255 citations