A proposal for a standardised protocol to barcode all land plants

Abstract

We propose in this paper to use three regions of plastid DNA as a standard protocol for barcoding all land plants. We review the other markers that have been proposed and discuss their advantages and disadvantages. The low levels of variation in plastid DNA make three regions necessary; there are no plastid regions, coding or non‐coding, that evolve as rapidly as mitochondrial DNA generally does in animals. We outline two, three‐region options, (1) rpoC1, rpoB and 1matK or (2) rpoC1, matK and psbA‐trnH as viable markers for land plant barcoding.

Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach

“…The accuracy of species identification was estimated by comparing the sequences of 63 native plant species analyzed for two markers, psbA-trnH and trnL-trnF, through GenBank leading toward a standardized multilocus solution. Up to now, no single region has been shown to have the ability to resolve species identification to a higher taxonomic rank, and it is unlikely that other single markers exist that would [25][26][27][28][29]. Firstly, the study confirmed the success of our modified DNA extraction protocol, which excluded the liquid nitrogen step and also of the high degree of versatility in the applied set of primers.…”

“…The PCR products ranging from 268 to 740 bp (average 444 bp) for the psbA-trnH and from 173 to 608 bp (average 399 bp) for the trnL-trnF intergenic spacer (IGS) even if most of the amplicons ranged between 300 and 500 bp and between 370 and 460 bp, respectively. As reported by other authors, the psbA-trnH showed higher sequence size length variation among plant species belonging to the same genera, principally due to the presence of insertions and deletions [24][25][26]28]. For the marker trnL-trnF, size variation was observed especially between species belonging to different families but a slight variation also emerged between highly correlated species belonging to the same genera or family.…”

“…The intergenic spacer psbA-trnH is one of the most variable non-coding regions of the plastid genome in angiosperms (in terms of having the highest percentages of variable sites), meaning that it could ensure high level of species discrimination [24,28,[30][31][32][33]. The other intergenic spacer trnL-trnF has been found to be capable of detecting inter-and intraspecies variation in a range of botanical species and has been employed in several phylogenetic studies [34][35][36].…”

“…A portion of the mitochondrial cytochrome c oxidase I gene sequence is currently being used as a universal barcode in certain animal groups and has been proposed also in the forensic field [21][22][23]. Based on the existing literature, there is currently no available universally usable region, and it is generally agreed that a multilocus approach based on plastid (chloroplast) data is the most effective strategy for species identification and recognition in plants [24][25][26][27][28][29]. A variety of loci have been recently suggested as potential DNA barcodes in plants, in both the nuclear and plastid genomes [28][29][30][31][32][33].…”

“…Based on the existing literature, there is currently no available universally usable region, and it is generally agreed that a multilocus approach based on plastid (chloroplast) data is the most effective strategy for species identification and recognition in plants [24][25][26][27][28][29]. A variety of loci have been recently suggested as potential DNA barcodes in plants, in both the nuclear and plastid genomes [28][29][30][31][32][33]. Our laboratory has selected two regions of the chloroplast genome, psbA-trnH and trnL-trnF, frequently enclosed in different barcoding selections, to quantify how well these alleged barcoding regions work for a regional flora and for assessing the utility of barcoding markers for forensic investigations.…”