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.

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

“…However, plant‐plastid barcodes typically have lower resolving power to separate closely related plant species compared to the animal barcode, and in several cases, conspecifics or recently diverged species do not form highly supported, distinct sequence clusters that allow species discrimination (Hollingsworth et al., 2016; van Velzen, Weitschek, Felici, & Bakker, 2012; Zhang et al., 2012). In fact, a uniquely identified species in a given genus is the exception rather than the rule in most plant barcoding studies (Hollingsworth, Graham, & Little, 2011). For these reasons, standard plant barcodes are more appropriately used as “molecular augmentations” to preexisting herbarium identifications as the current plant barcode sequences do not contain sufficient variation to define a species‐level framework for every plant species (Hollingsworth et al., 2016).…”

“…Further, in using plant barcodes, it is important to understand the limited resolving power of the technique when formulating the objectives of a particular study (Hollingsworth et al., 2016). There are other practical issues to consider which include but are not limited to, the requirement for species‐specific primer combinations which directly determines recovery of matK sequences, DNA extraction methods for recalcitrant species whose genomic DNA may be contaminated with PCR inhibitors, for example, muco‐polysaccharides, proteins, polyphenols, and tannins, the need for and expense involved in automated DNA extraction for high‐throughput processing of large sample sizes, and the difficulty in constructing reference sequence datasets or libraries (Hollingsworth et al., 2011, 2016). The most recent development in plant DNA barcoding is to sequence the complete chloroplast genome which will be used as a “super‐barcode” in order to overcome some of the issues associated with low resolving power of the single or multiple loci barcode approach (Hollingsworth et al., 2016; Li et al., 2015).…”

Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species

“…This is related to the fact that plant mitochondrial genes appeared to be unsuitable markers for DNA barcoding (Kress et al 2005). Moreover, there is probably no single marker in the plant genome that exhibits all features required for DNA barcoding (Hollingsworth et al 2011). Therefore, two chloroplast loci that meet the requirements for DNA barcoding only partially were chosen for species identification among the land plants, these are: the fastevolving matK (about 700 bp) and the slowly evolving rbcL (about 500 bp) (CBOL Plant Working Group 2009).…”

Resolving phylogenetic relationships and species delimitations in closely related gymnosperms using high-throughput NGS, Sanger sequencing and morphology

“…As a consequence, NGS has allowed for the description of a rapidly increasing number of nuclear, mitochondrial and plastid genomes (Rounsley et al 2009;Deschamps and Campbell 2010) and is set to contribute to a deeper understanding of both phylogeny and evolution in many lineages. Among the three types of genomes, data of entire plastid genomes have been widely used to seek for markers for the purpose of DNA barcoding (Hollingsworth et al 2011;Nock et al 2011), to investigate population genetics, and in phylogeographic studies (Powell et al 1995;Provan et al 2001;Mariac et al 2014), as well as to efficiently address phylogenetic questions in both angiosperms (Jansen et al 2007;Moore et al 2011;Huang et al 2014) and gymnosperms (Parks et al 2009;Lin et al 2010;Yi et al 2015). Here, we use data from NGS, combined with data from traditional Sanger sequencing and morphology, with the primary aim of resolving the phylogeny and species delimitation among Chinese lianoid species of Gnetum L. (Gnetales).…”