Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding

By P. Taberlet, É. Coissac, F. Pompanon, Ludovic Gielly, C. Miquel, A. Valentini, T. Vermat, G. Corthier, C. Brochmann, Eske Willerslev. Nucleic Acids Research, 2006

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DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254–767 bp) and of a shorter fragment of this intron (the P6 loop, 10–143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8f444ec7042bb5f782740d1f70e1f5feba426146

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Citations in the corpus

A DNA barcode for land plants (2009, background): “In the short term, where further resolution and universality are required, we envisage that the core rbcL matK barcode will be augmented in individual projects from a f lexible short-list of supplementary loci including the noncoding plastid regions examined here (trnH– psbA, atpF–atpH, and psbK–psb”
Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus) (2015, methodology): “Our results contrast with those of Thomsen et al. (2012) who found a positive correlation between DNA concentration and estimated population density based on conventional monitoring.”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, background): “150 bp) P6 loop of the trnL intron (Taberlet et al. 2007; Ando et al. 2013, 2016) is the preferred target.”
Choosing and Using a Plant DNA Barcode (2011, background): “This very short ‘minibarcode’ has proved very useful to ecologists studying highly degraded DNAs and using next generation sequencing technologies to assess the diversity of complex environmental samples (e.g. faeces; [45]).”
Persistence of Environmental DNA in Freshwater Ecosystems (2011, methodology): “using ecoPCR software [14]) in order to insure primer specificity (e.”
Who is eating what: diet assessment using next generation sequencing (2012, background): “At the same time, there has been a massive expansion of sequence databases through the DNA barcoding of animals and plants (Hebert et al. 2003; Chase et al. 2007; Taberlet et al. 2007), without which accurate interpretation of the thousands of sequences generated by NGS would be impossible (Valentin”
The Arctic – an evolutionary freezer? (2008, background): “2007 ; JH Sonstebo, C Brochmann, AK Brysting et al.”
Towards next‐generation biodiversity assessment using DNA metabarcoding (2012, background): “Nevertheless, suitable metabarcoding markers have been relatively easy to find, for example, for vascular plants and bryophytes (Taberlet et al. 2007; Epp et al. submitted), vertebrates (Riaz et al. 2011; Shehzad et al. 2012), birds (Epp et al. submitted), earthworms (Bienert et al. 2012) and fungi…”
Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well (2008, background): “‘‘universal plastid amplicon’’ or UPA [13]), and the plastid trnL– trnF intergenic spacer [14] have been proposed.”
Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus (2012, methodology): “2008): before the eDNA analysis, primer reliability, robustness and specificity were tested, first in silico [using ecopcr software (Taberlet et al. 2007)] and then on high-quality DNA (extracted from tissues samples), and PCR conditions were optimized (Ficetola et al.”
New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study (2011, methodology): “The PCR products obtained were sequenced on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA) using standard protocols (Taberlet et al. 2007).”
An update on chloroplast genomes (2008, background): “In a similar study, Taberlet et al. (2007) evaluated the utility of trnL (UAA) intron for barcoding purposes.”
DNA barcoding for ecologists. (2009, background): “(DNA barcoding sensu stricto), whereas ecologists working with environmental samples will favor criteria (iv) and (v) (DNA barcoding sensu lato) [ 69 ].”
Evaluation of 10 plant barcodes in Bryophyta (Mosses) (2010, background): “Other suggested loci include rbcL (Newmaster et al., 2006), the chloroplast trnL intron (Taberlet et al., 2007), and three regions proposed by Ki-Joong Kim, atpF-atpH , matK, and psbK-psbI (Pennisi, 2007).”
Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems (2016, methodology): “This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. can limit the level to which taxonomic assignments can be made (e.g. Taberlet et al. 2006).”