Abstract
Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation—especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.
Highlights
Barcoding all described species is an enormous task with large sums being spent annually toward this end [1]
The primer pairs chosen using Ceratozamia hildae and Cycas ophiolitica (Figure 1) for ndhJ, rpoB and matK did not work well for the remaining taxa (Table 1): non-specific primer binding resulted in multiple bands or complete lack of amplification
A recently posted Phase II update based on research from the Plant Working Group indicates a new primer pair for matK that was successful in Encephalartos and may be successful across all genera of cycads, while YCF5 was determined to not be suitable as a barcode region for all land plants due to its apparent absence in bryophytes
Summary
Barcoding all described species is an enormous task with large sums being spent annually toward this end [1]. Proponents argue that molecular barcodes can be used to identify new species and eliminate the need for the complex taxonomic training that is currently required for species description and identification [9]—helping to ease the taxonomic crisis, especially in countries with high biodiversity and small numbers of practicing taxonomists. Barcodes are appealing as a powerful tool to identify already described species, the cautious among us argue that the use of a single locus for identification may produce misleading results especially considering the different evolutionary histories of organellar and nuclear genomes within a single species [11]. Others reject the use of barcodes for taxonomic purposes on the grounds that species description and identification requires full taxonomic revisions and that ‘phylogenies’ produced by barcoding genes do not necessarily represent evolutionary history [2,12]
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