Abstract
DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.
Highlights
In recent years, DNA barcoding has been proposed as a method to survey biodiversity in the field (Hebert et al, 2003; Gross, 2012)
Sequence and species count for both 2–20 and 5–20 datasets are presented in Table 2, showing the highest number of genera and species for markers trnL, RuBisCO large subunit (rbcL), and maturase K (matK)
RbcL was the marker with the highest number of sequences and species available in databases after quality control and filtering (Table 2, 2–20 dataset)
Summary
DNA barcoding has been proposed as a method to survey biodiversity in the field (Hebert et al, 2003; Gross, 2012). DNA barcoding represents an efficient tool for the identification of cryptic or invasive species (Lopez-Vaamonde et al, 2021), conservation, and community ecology (Hollingsworth et al, 2011; Yessoufou et al, 2013; Bezeng et al, 2017). This tool is based on the conserved DNA biomarkers with more interspecific than intraspecific variability creating a barcoding gap (Candek and Kuntner, 2015), which allows the possibility to identify an organism at different taxonomic levels. Examples of these are the 16S rRNA gene in prokaryotes, the Internal Transcribed Spacer (ITS) region in fungi and the Cytochrome Oxidase I
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