Land plants challenge standardized DNA-based identification. Different groups of land plants are deeply divergent at the DNA level, yet there are relatively few sequence differences among closely-related species. Deep divergences make it difficult to design broad-range primers that amplify DNA from the many kinds of plants, and small differences among closely-related species mean longer sequences are needed to distinguish them. Plant mitochondrial genes including COI evolve too slowly to be useful. The best strategy appears likely to be a combination of 2 or 3 gene regions from the chloroplast genome. Chloroplasts are organelles which house the plants’ photosynthetic machinery and have their own genome, like mitochondria.
In May 2007 Taxon, 19 researchers from 12 institutions in 7 countries (Brazil, Colombia, Denmark, Mexico, South Africa, U.K. and U.S.A.) report on tests of candidate barcode regions. Chase and co-investigators outline the rationale and results for selecting and testing potential land plant barcode regions. The finalists were winnowed down from more than 100 coding and non-coding regions in chloroplast DNA by testing 96 pairs of closely-related plant species to see which regions could be amplified and provide discrimination. Although the actual data are not shown in this short update, they summarize their results by proposing three chloroplast gene regions as a standard barcode for land plants: two coding regions, matK and rpoC1, and, either a third coding region, rpoB, or the non-coding psbA-trnH spacer region.
In June 2007 PLoS ONE, Kress and Erikcson, Smithsonian Institution, examine nine potential loci (8 plastid regions which includes the four final candidates in the Taxon paper, and nuclear gene ITS). In this analysis, as in Chase et al report, there are two steps: first, does the region amplify with a standard set of primers, and second, if so, does the sequence enable discrimination of closely-related species. In the 48 pairs of species examined, only two loci, trnH-psbA and rbcL-a exhibited more than 90% success with standard primers. Based on this admittedly small sample, the authors propose a “two-locus global DNA barcode for land plants” in which “rbcL-a provides a strong recognition anchor that will place an unidentified specimen into a family, genus, and sometimes species; the highly variable trnH-psbA spacer will futher narrow the corrrect species identification where rbcL-a lacks discrimination power.”
These are promising starts towards a standardized DNA barcode for land plants. More tests are needed, including analysis of variation within species, as both studies used single specimens for each target species.
This is extremely interesting, was this done via haplotype mapping or is this only possible in animals?
Standards for DNA barcoding of land plants will be announced in Proc Natl Acad Sci USA in July 2009.