Choosing and using a plant DNA barcode

Abstract

The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.

Figure 1. Schematic timeline of the consideration of different markers as plant barcodes.

Colours (red = warm; blue = cool) represent an informal measure of enthusiasm among DNA barcoding researchers in the systematics community for CBOL and iBOL adoption of different markers. The different shading of trnL (P6) reflects the parallel use of the P6 loop for DNA profiling of degraded DNAs in ecological studies (see text). * = the two markers that form the core-barcode for land plants. rbcL a is used in this figure to distinguish this shorter barcode region of the gene proposed by Kress and Erikson and the full length (ca. 1400 bp) gene sequence of rbcL. Elsewhere in the text, when we refer to rbcL we are referring to the short barcode region. The dashed lines indicate the timing of three international barcoding conferences in London (2005), Taipei (2007) and Mexico City (2009). The consideration of the different markers as barcodes are from the following sources: Kress et al. , Chase et al. , Chen et al. , Kew consortium , , Kim et al. see , Lahaye et al. , Newmaster et al. , Kress and Erickson , Taberlet et al. , Presting et al. .

Figure 2. Schematic representation of the impacts of intra-specific gene flow on species discrimination success.

Parts (A) and (B) each represent two species (one shades of red, one shades of blue), each consisting of three populations. The black line between the species indicates a barrier to gene flow, with the thickness of the line indicating the strength of the barrier. In (A) intra-specific gene flow among populations is high (indicated by the vertical arrows). Thus, where gene flow occurs between species (wavy arrow), there is a barrier to extensive neutral introgression because establishment of immigrant alleles is prevented by a regular influx of conspecific alleles from other populations. In (B) intra-specific gene flow among populations is low. Thus populations are more differentiated from one another and are less likely to show taxon-specific barcode markers. In addition, the flux preventing establishment of introgressed alleles is lower because it involves only alleles in the (middle) recipient population and not the other populations of the ‘blue’ species.