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From:
Loraine Kohorn <[log in to unmask]>
Reply To:
- JBS-L - Josselyn Botanical Society discussion list of the University of Maine <[log in to unmask]>
Date:
Tue, 12 Feb 2008 21:39:21 -0500
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>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.

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