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Botanical identities

February 4, 2008 By Heidi H Ledford This article courtesy of Nature News.

DNA barcoding for plants comes a step closer.

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Researchers have used a DNA sequence to distinguish between more than 1,600 botanical samples from two biodiversity hotspots, providing the largest test yet of ‘DNA barcoding’ in plants.

But this will not end the ongoing debate over which barcodes botanists should adopt. “I think this is a step forward,” says John Kress of the Smithsonian Institution’s National Museum of Natural History in Washington DC. “But I don’t think it means we’re there yet.”

DNA barcodes are sequences that vary extensively between species but hardly at all within them, and so can be used to distinguish one species from another. Established barcodes could be used to quickly inventory biodiversity in a protected area, for example, or to monitor shipments of plants for illegal trading of endangered species.

Establishing a barcode for animals has been fairly easy; part of a gene called CO1, which has been used for years to study animal family trees, fulfils the requirements well. But plants have been more problematic. Labs around the world have churned out paper after paper supporting various alternatives to CO1. Each lab designed its experiments differently and tested its barcodes on different sets of plants. Some moved ahead on large-scale projects using their favoured barcodes regardless of the field’s lack of consensus.

“It’s a very contentious issue,” says Kenneth Cameron, director of the Wisconsin State Herbarium at the University of Wisconsin-Madison. “There are a lot of politics and personalities involved.”

It was against this background that Vincent Savolainen of the Royal Botanic Gardens, Kew in London decided to compare some of the leading barcode candidates across a large set of samples. As they report this week in Proceedings of the National Academy of Sciences, he and his colleagues tested samples from 86 species from southern Africa and Costa Rica using eight barcodes (R. Lahaye et al. Proc. Natl Acad. Sci. USA doi:10.1073/pnas.0709936105 ; 2008).

The researchers found that barcodes from genes called matK and trnH-psbA, used either alone or together, correctly classified just over 90% of the species. Because trnH-psbA sequences can be difficult to compare across species, they went on to inventory another 1,036 species of orchid using matK alone.

But this does not make matK the uncontested champ. For one thing, researchers have reported difficulty amplifying the gene for sequencing in some plants. Savolainen says his team used an improved amplification protocol, but Kress says the new method still fails with some species. And a better idea of the technique’s range is needed: it may do well with orchids, but what of liverworts or ferns?

Most suspect that, in the end, a single barcode will not suffice. At a meeting of the Consortium for the Barcode of Life in Taipei, Taiwan, last autumn, the Plant Working Group proposed three barcodes: matK, trnH-psbA and another called atpF-H. Savolainen and his team think matk and trnH-psbA may suffice.

The next step will be a test of all the leading barcodes against 675 species of plants. This test is being coordinated by Peter Hollingsworth of the Royal Botanic Gardens in Edinburgh, UK, who runs the barcode consortium’s Plant Working Group. It will study the reproducibility of results in different labs, with the outcome expected in April. Kress is optimistic that this may lead to a consensus, but acknowledges that the delays and bickering have been frustrating. “I’m beginning to think I’m going to start working on fruitflies,” he jokes.

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