>Date: Tue, 12 Feb 2008 16:44:00 -0500 >From: david duthie <[log in to unmask]> >To: bioplan <[log in to unmask]>, Cathy Maize <[log in to unmask]>, > Gillian Chalmers <[log in to unmask]> >Subject: [bioplan] DNA 'barcode' identified for >plants, and working for amphibians, but maybe not for corals > > >Dear BIOPLANNERS, > >Dan Janzen`s vison of a hand-held scanner that >will read the DNA "barcode" a biological >specimen in the field and then, via the >internet link to the world`s collective >information on that species is slowly becoming reality. > >Today, three "barcode" articles crossed my desk >(see below) and this prompted me to follow a few links. > >The Barcode of Life Initiative will provide you >with as much, perhaps more, than you could ever want to know about barcoding! > >http://www.dnabarcodes.org/pa/ge/what_is_boli > >Best wishes > >David Duthie > >-- >David Duthie >UNEP-GEF Biosafety Unit >Geneva >Email: david.duthie @ unep.ch > >********************************************** >February 6, 2008 > >DNA 'barcode' identified for plants > >A 'barcode' gene that can be used to distinguish between the majority of >plant species on Earth has been identified by scientists who publish >their findings in the Proceedings of the National Academy of Sciences >journal. > >This gene, which can be used to identify plants using a small sample, >could lead to new ways of easily cataloguing different types of plants >in species-rich areas like rainforests. It could also lead to accurate >methods for identifying plant ingredients in powdered substances, such >as in traditional Chinese medicines, and could help to monitor and >prevent the illegal transportation of endangered plant species. > >The team behind the discovery found that DNA sequences of the gene >'matK' differ among plant species, but are nearly identical in plants of >the same species. This means that the matK gene can provide scientists >with an easy way of distinguishing between different plants, even >closely related species that may look the same to the human eye. > >The researchers made this discovery by analysing the DNA from different >plant species. They found that when one plant species was closely >related to another, differences were usually detected in the matK DNA. > >The researchers, led by Dr Vincent Savolainen, dual appointee at >Imperial College London's Department of Life Sciences and the Royal >Botanic Gardens, Kew, carried out two large-scale field studies: one on >the exceptionally diverse species of orchids found in the tropical >forests of Costa Rica, and the other on the trees and shrubs of the >Kruger National Park in South Africa. Dr Savolainen and his colleagues >in the UK worked alongside collaborators from the Universities of >Johannesburg and Costa Rica who played a key role in this new discovery. > >Using specimens collected from Costa Rica, Dr Savolainen and colleagues >were able to use the matK gene to identify 1,600 species of orchid. In >the course of this work, they discovered that what was previously >assumed to be one species of orchid was actually two distinct species >that live on different slopes of the mountains and have differently >shaped flowers adapted for different pollinating insects. > >In South Africa the team was able to use the matK gene to identify the >trees and shrubs of the Kruger National Park, also well known for its >big game animals. > >Dr Savolainen explains that in the long run the aim is to build on the >genetic information his team gathered from Costa Rica and South Africa >to create a genetic database of the matK DNA of as many plant species as >possible, so that samples can be compared to this database and different >species accurately identified. > >"In the future we'd like to see this idea of reading plants' genetic >barcodes translated into a portable device that can be taken into any >environment, which can quickly and easily analyse any plant sample's >matK DNA and compare it to a vast database of information, allowing >almost instantaneous identification, " he says. > >Although Dr Savolainen concedes that such technological applications may >be some years away from realisation, he says the potential uses of the >matK gene are substantial: "There are so many circumstances in which >traditional taxonomic identification of plant species is not practical - >whether it be at ports and airports to check if species are being >transported illegally, or places like Costa Rica where the sheer >richness of one group of plants, like orchids, makes accurate >cataloguing difficult." > >The matK gene may not, however, be able to be used to identify every >plant species on Earth. In a few groups of species, additional genetic >information may be required for species-level identification because >hybridization - where species cross-breed and genetic material is >rearranged - may confuse the information provided by matK. > >This research was funded by the Defra Darwin Initiative, the >Universities of Johannesburg and Costa Rica, the South African National >Research Foundation, the Royal Botanic Gardens, Kew, and the Royal Society. > >Joan Ruddock, Minister for Climate Change and Biodiversity said: "This >is a great breakthrough that could save many endangered plants. The >Defra-funded Darwin Initiative has a reputation for producing real and >lasting results and I congratulate everyone involved in this project >which could have huge benefits for plant identification and conservation >in the future." > >Contact: >Danielle Reeves >[log in to unmask] >44-020-759-42198 >Imperial College London > > >Source: EurekAlert > >*********************************************** > >M. ALEX SMITH, NIKOLAI A. POYARKOV JR, PAUL D. N. HEBERT (2008) >CO1 DNA bar-coding amphibians: take the chance, meet the challenge >Molecular Ecology Resources 8 (2), 235246. >doi:10.1111/j.1471-8286.2007.01964.x > >Abstract > >Although a mitochondrial DNA barcode has been >shown to be of great utility for species >identification and discovery in an increasing >number of diverse taxa, caution has been urged >with its application to one of the most >taxonomically diverse vertebrate groups — the >amphibians. Here, we test three of the perceived >shortcomings of a CO1 DNA barcode's utility with >a group of Holarctic amphibians: primer fit, >sequence variability and overlapping intra- and >interspecific variability. We found that >although the CO1 DNA barcode priming regions >were variable, we were able to reliably amplify >a CO1 fragment from degenerate primers and >primers with G-C residues at the 3' end. Any >overlap between intra- and interspecific >variation in our taxonomic sampling was due to >introgressive hybridization (Bufo/Anaxyrus), >complex genetics (Ambystoma) or incomplete >taxonomy (Triturus). Rates of hybridization and >species discovery are not expected to be greater >for amphibians than for other vertebrate groups, >and thus problems with the utility of using a >single mitochondrial gene for species >identification will not be specific to >amphibians. Therefore, we conclude that there is >greater potential for a CO1 barcode's use with >amphibians than has been reported to date. A >large-scale effort to barcode the amphibians of >the world, using the same primary barcode region >of CO1, will yield important findings for science and conservation. > > >*********************************************** > >T. L. SHEARER, M. A. COFFROTH (2008) Barcoding >corals: limited by interspecific divergence, not >intraspecific variation. Molecular Ecology >Resources 8 (2), 247255. doi:10.1111/j.1471-8286.2007.01996.x > >Abstract > >The expanding use of DNA barcoding as a tool to >identify species and assess biodiversity has >recently attracted much attention. An attractive >aspect of a barcoding method to identify >scleractinian species is that it can be utilized >on any life stage (larva, juvenile or adult) and >is not influenced by phenotypic plasticity >unlike morphological methods of species >identification. It has been unclear whether the >standard DNA barcoding system, based on >cytochrome c oxidase subunit 1 (COI), is >suitable for species identification of >scleractinian corals. Levels of intra- and >interspecific genetic variation of the >scleractinian COI gene were investigated to >determine whether threshold values could be >implemented to discriminate conspecifics from >other taxa. Overlap between intraspecific >variation and interspecific divergence due to >low genetic divergence among species (0% in many >cases), rather than high levels of intraspecific >variation, resulted in the inability to >establish appropriate threshold values specific >for scleractinians; thus, it was impossible to >discern most scleractinian species using this gene.