Selection of candidate coding DNA barcoding regions for use on land plants

Ford, Caroline S.; Ayres, Karen L.; Toomey, Nicola H.; Haider, Nadia; Stahl, Jonathan Van Alphen; Kelly, Laura J.; Wikström, Niklas; Hollingsworth, Peter M.; Duff, R. Joel; Hoot, Sarah B.; Cowan, Robyn S.; Chase, Mark W.; Wilkinson, M. J.

doi:10.1111/j.1095-8339.2008.00938.x

Cited by 261 publications

(204 citation statements)

References 36 publications

(61 reference statements)

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“…A number of studies have assessed the advantages and limits of the various gene regions available for plant DNA barcoding (CBOL Plant Working Group 2009;Ford et al 2009;Hollingsworth et al 2009Hollingsworth et al , 2011Chen et al 2010). In an effort to standardize DNA barcoding methods, the chloroplast regions rbcL and matK were selected as barcode markers, based on their relative universality and combined taxonomic resolution (CBOL Plant Working Group 2009;Hollingsworth et al 2011), although ITS2 has also been recommended as a standard barcode for plant DNA barcoding based on its higher taxonomic resolution (Chen et al 2010).…”

Section: Component 2: Genetic Markersmentioning

confidence: 99%

Pollen DNA barcoding: current applications and future prospects

Bell

Vere

Keller

et al. 2016

Genome

205

170

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Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.Key words: DNA metabarcoding, metagenomics, pollen, palynology, high-throughput sequencing, next-generation sequencing.Résumé : L'identification de l'espèce à l'origine d'un pollen se prête à de nombreuses applications dont la description des réseaux plante-pollinisateur, la reconstruction de communautés de plantes anciennes, l'authentification de produits, la surveillance des allergènes et les enquêtes médicolégales. Cependant, ces applications ont précédemment été limitées à l'identification du pollen par examen microscopique, un processus lent, à faible résolution taxonomique et qui compte peu de praticiens experts. Une alternative est l'identification du pollen par le recours aux codes à barres de l'ADN, une avenue qui permettrait de surmonter plusieurs de ces limitations. De récentes études ont montré qu'il était possible d'amplifier les marqueurs de codage tant chloroplastiques que nucléaires à partir du pollen. Ces récentes validations du métacodage à barres chez le pollen indiquent qu'il est maintenant opportun pour les chercheurs dans divers domaines de considérer l'emploi de ces méthodes dans leurs programmes de recherche. Dans cet article, les auteurs passent en revue le domaine naissant du codage à barres du pollen et discutent des nouvelles applications potentielles de cette technologie en mettant en lumière les limitations existantes ainsi que de futurs développements qui pourraient accroître son utilité dans un grand nombre d'applications. [Traduit par la Rédaction] Mots-clés : métacodage à barres, métagénomique, pollen, palynologie, séquençage à haut débit, séquençage de nouvelle génération.

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Section: Component 2: Genetic Markersmentioning

confidence: 99%

Pollen DNA barcoding: current applications and future prospects

Bell

Vere

Keller

et al. 2016

Genome

205

170

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“…have been studied and validated, and were recommended as possible barcode loci (Kress et al 2005;Chase et al 2007;Ford et al 2009;Pennisi 2007). A pair of such recommended sequences are segments of two plastid genes, ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL), and maturase K (matK).…”

Section: Introductionmentioning

confidence: 99%

Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants

et al. 2017

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DNA barcoding of United Arab Emirates (UAE) native plants is of high practical and scientific value as the plants adapt to very harsh environmental conditions that challenge their identification. Fifty-one plant species belonged to 22 families, 2 monocots, and 20 eudicots; a maximum number of species being legumes and grasses were collected. To authenticate the morphological identification of the wild plant taxa, rbcL and matK regions were used in the study. The primer universality and discriminatory power of rbcL is 100%, while it is 35% for matK locus for these plant species. The sequences were submitted to GenBank; accession numbers were obtained for all the rbcL sequences and for 6 of matK sequences. We suggest rbcL as a promising barcode locus for the tested group of 51 plants. In the present study, an inexpensive, simple method of identification of rare desert plant taxa through rbcL barcode is being reported.

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“…The matK primer sets of Ford et al (2009) and rbcLa primers of Levin et al (2003) and Kress and Erickson (2007) were used for PCR amplification and sequencing amplification. DNA sequences were obtained using an Applied Biosystems 3130 Genetic Analyser.…”

Section: Methodsmentioning

confidence: 99%

Assessing Clivia taxonomy using the core DNA barcode regions, matK and rbcLa

Spies¹,

Spies²

2018

Bothalia

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Background: Clivia is a genus of the family Amaryllidaceae endemic to South Africa and Swaziland. Six species and one natural hybrid have been described. Some morphological traits overlap between some species, thus causing taxonomic confusion.Objectives: The discriminatory power of the core DNA barcodes (matK and rbcLa) was evaluated, and the current taxonomy of Clivia was assessed.Method: Seventy-four two-locus DNA barcodes from 4 to 18 specimens per species were generated.Results: The matK region had a higher mean intraspecific variation of 0.21 compared with the 0.02 of rbcLa. The two-locus barcodes have an aligned length of 1335 base pairs. Three species, Clivia mirabilis, Clivia nobilis and Clivia caulescens, are monophyletic in the Bayesian Inference (BI) cladogram. The remaining Clivia species (Clivia miniata, Clivia gardenii, Clivia robusta and their affinities) are paraphyletic. Clivia is divided into 17 haplogroups with those of C. mirabilis and C. nobilis being unique. Clivia caulescens has three haplotypes. The Clivia species from the north-eastern distribution range of the Eastern Cape and KwaZulu-Natal provinces have 11 haplogroups and no species-specific DNA barcodes. These groups have no correlation with the current taxonomy or geographical distribution.Conclusions: Only 37.33% of the species can be correctly identified with the ‘best match’ option in SpeciesIdentifier. Clivia mirabilis, C. nobilis and C. caulescens have unique DNA barcodes to identify them. Specimens from the Ngome area in KwaZulu-Natal have a unique DNA barcode, separating them from the rest of C. gardenii. A taxonomic revision is suggested.

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Selection of candidate coding DNA barcoding regions for use on land plants

Cited by 261 publications

References 36 publications

Pollen DNA barcoding: current applications and future prospects

Pollen DNA barcoding: current applications and future prospects

Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants

Assessing <i>Clivia</i> taxonomy using the core DNA barcode regions, <i>matK</i> and <i>rbcLa</i>

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