Land plants and DNA barcodes: short-term and long-term goals

Abstract

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL, trnL-F, etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the 'genetic gaps' that are useful in assessing species limits.

Prospects for fungus identification usingCO1DNA barcodes, withPenicilliumas a test case

“…Early work on marine algae (16) revealed that CO1-based systems are promising for this group. In contrast, this gene will be less effective for land plants because of their slower mitochondrial evolution, and efforts are underway to identify alternate gene regions that will deliver species-level resolution (17)(18)(19). The potential effectiveness of CO1 in species identification of fungi has not yet been evaluated, and the present study represents a first step to address this gap.…”

DNA barcoding of arid wild plants using rbcL gene sequences

“…However, the universality of barcode markers is hampered due to morphological/geographical variation and reticulate evolution in plant species (Roy et al, 2010). The ongoing research on plant barcoding suggests that the development of universal DNA barcoding markers for land plants is challenging; even the choice of the correct loci has been debated (Chase et al, 2005;Kress et al, 2005;Fazekas et al, 2008;de Groot et al, 2011). Arguments about the selected core loci for plant barcoding are related to the lack of discriminatory power and/or primer universality (Roy et al, 2010).…”

Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications

“…It is admittedly uncertain how well cox1-5 0 will function for species discrimination in the other kingdoms of life because the mode of inheritance, rate of divergence, as well as many of the other attributes discussed above for this marker, are poorly known outside of the animals and land plants. For the latter, it was established that mitochondrial genes are generally more slowly evolving than in animals (Barkman et al 2000), but that the more rapidly evolving plastid genome may provide sequences that would be adequate candidates for genetic barcoding (Chase et al 2005). As for the many unicellular and multicellular protists, little is known and only through exploratory research will the utility of cox1-5 0 as a genetic marker be established for the various lineages.…”