NEW YORK (GenomeWeb News) – An international research team has identified a pair of sequences that they say are the best candidates so far for barcoding land plants.
In a paper scheduled to appear online this week in the Proceedings of the National Academy of Sciences, the researchers examined more than 900 samples representing in excess of 500 plant species, looking for a sequence that satisfied barcode criteria established by the Consortium for the Barcode of Life, or CBOL. After putting the seven loci through their paces, they concluded that two — rbcL and matK — could accurately classify more than 70 percent of land plant species while putting the remaining species in the correct group of related species.
"We've selected areas of DNA that are available in the vast majority of plants, could easily and accurately be sequenced, and when combined, provide a near-unique signature for barcoding," co-author Sean Graham, a botanist at the University of British Columbia, said in a statement.
For most animals, researchers can glean barcode information from the sequence of a mitochondrial gene called CO1. But so far there has been little agreement on which bits of DNA should be used to classify the estimated 400,000 species of land plants on the planet.
"In plants … low substitution rates of mitochondrial DNA have led to the search for alternative barcoding regions," the authors explained. "Different research groups have proposed various combinations of these loci as their preferred plant barcodes, but no consensus has emerged. This lack of an agreed standard has impeded progress in plant barcoding."
For instance, last year, a team of British researchers published a paper in PNAS in which they used a bit of the plastid gene matK as a barcode to distinguish between more than 1,000 orchid species and identify previously unrecognized species. The lead author on that paper, Royal Botanic Gardens researcher Vincent Savolainen, is also a co-author on the current paper.
To try to hone in on loci for standardizing plant barcodes, the researchers tested the barcoding promise of seven different plastid genes using 907 plant samples from several different laboratories representing 445 angiosperm species, 38 gymnosperms, and 67 cryptogams.
The team assessed each potential barcode using data standards and locus selection criteria developed by CBOL, looking at qualities such as universality, sequence quality, and species discrimination.
Based on the subsequent experiments, the researchers narrowed down their search to three loci: trnH-psbA, rbcL, and matK. The authors noted that all three "possess attributes that are highly desirable in a plant DNA barcoding system, although none of the [three] loci fits all [three] criteria perfectly."
In the end, though, the team settled on rbcL and matK — loci that, together, could discern the correct plant species about 72 percent of the time and that placed the remaining species into their appropriate congeneric group.
And while these barcoding loci may eventually be refined, those involved say that the implementation of standard land plants barcodes will not only spur work on classifying land plants but may also aid in conservation efforts.
"The broad community agreement presented here, to sequence rbcL and matK as a standard [two]-locus barcode, is … an important step in establishing a centralized plant barcode database as a tool for taxonomy, conservation, and the multitude of other applications that require identification of plant material," the authors concluded.