Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well

Abstract

A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples). The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF–atpH, and psbK–psbI) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (trnH-psbA) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85–100% for plastid loci), with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (matK, psbK–psbI, trnH-psbA) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69–71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

“…Others explained amplification failure as a result of poor annealing with standard matK or rbcL primers and highlighted the need to redesign species‐specific primers (Kress & Erickson, 2007; Sass et al. 2007; Fazekas et al., 2008; Lahaye et al., 2008; Casiraghi et al., 2010; Roy et al., 2010). According to Casiraghi et al.…”

“…For example, matK and rbcL were able to identify species to the Betus and Salix genus level, but did not allow adequate resolution to distinguish among species belonging to these genera and the rate of amplification was low (only 21% of the Salix samples amplified; Jarvinen et al. 2004; Fazekas et al., 2008; von Crautlein et al., 2011). …”

Phylogenetic Analysis of Pines Based on Chloroplast trnT-trnL Intergenic Spacer DNA Sequences

“…The technique can be performed using small parts of the organism, so it overcomes the limitation of morphological classification (Hollingsworth et al 2009). In this technique, non-coding regions of DNA are particularly important, as they tend to have the most variation (Fazekas et al 2008). DNA barcoding technology is being used for various purposes in the tree industry.…”

Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences

“…Given the limitations, an increasing number of studies showed that plant species identification is unlikely accurate and different combinations have been proposed (Fazekas et al, 2008; Kress and Erickson, …”

“…rbcL is the most commonly sequenced gene by plant systematists for phylogenetic purposes, followed by the trnL-F intergenic spacer, matK, ndhF, and atpB (Shaw et al, 2005;Soltis et al, 2001). Additionally, psbA-trnH, rpoB, rpoC, atpFatpH, psbK-psbI, or a combination of several regions has been selected as candidate regions in the chloroplast (Fazekas et al, 2008;Kress et al, 2005;Ma et al, 2010). In the nuclear genome, most single-copy genes, as well as their introns, have been excluded as barcode candidates because of the lack of universal primers for their amplification.…”