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Identifying World's Species With Genetic Bar Codes
Fokker writes "Reuters reports that scientists from around the world launched a project on thursday to genetically identify species using bar codes. By taking a snippet of DNA from all the known species on Earth and linking them to photographs, descriptions and scientific information, the researchers plan to build the largest database of its kind."
I work in this lab. Specifically, I'm working on objective analysis of RNA sequence alignment heuristics.
...actually finding and agreeing on the locus (piece of DNA) to use for this. It has to be present in all species, i.e. in gnat and cow and jellyfish, but also has to be variable enough to be able to differenciate between, for example, the Tennesse gnat and Alabama gnat.
The main problem is that the locus must contain two regions to the right and to the left of the sequence of interest that must be highly invariable. This is necessary so that the same PCR primers can be used to amplify the sequence in most species. The amplification step is necessary for sequencing.
i wonder which specific DNA sequence they use, since it should be present in all species and sufficiently divergent to discriminate between species.
another thing that might be problematic, is the dicrepancy between different classification methods... sometimes morphological or biochemical classifications do not coincide with DNA based classifications.
i like the effort, but i have to see it work before i am convinced of the merits. the article is a bit vague regarding implementation.
The region of DNA they are using as a barcode is a 561 bp stretch of the cox1 gene, which encodes Cytochrome C Oxidase subunit 1.
The gene is found in the mitochondrial DNA in all animals and plants, and many homologues are in bacteria and other forms of life.
There are some great resources out there
http://barcodinglife.com/, The official site.
Or for the geeky, http://www.ncbi.nlm.nih.gov/, GenBank, search for cox1, it's the second most sequenced gene on the planet,
you'll find it's sequence and other info you can play with 'bioinformatically'.
If anyone is interested Cytochrome C Oxidase is the final protein in your electron transport chain.
It is the enzyme that reduces oxygen in your body (try breathing in!), and is found in 'nearly' all life that lives in oxygen.
Mike Jones-{ Genetic Engineer, in Training }-
The fragment of DNA that they are sequencing is located on the mitochondria and is part of the cytochrome c oxidase gene (COI). http://en.wikipedia.org/wiki/DNA_barcode
I am a taxonomist and can tell you this is of limited usefulness, sure we will be able to see some differences between organisms, but this is already done is many studies with the control region of the mitochondria.
The problem could be if people just rely on these sequences alone to delineate species, we learnt this years ago in bacterial taxonomy that you simply cannot rely on any one particular gene (There is evidence of horizontal gene transfer in 16S genes if someone was going to counter with that).
A speciation event is driven by some environmental pressure (change in temperature say). The genes that are under selection of this pressure will change at different rates to one under no direct pressure (COI).
I could rant on but, I think this project is of some use only if combined with traditional taxonomy. The danger is that a large flashy project like this will steal research dollars away from traditional taxonomy.
You can perfectly well compare the sequence of two homologous genes from two species and knowing the function of one you can guestimate the function and domains of the other.
Life is what happened when Good Intentions met Harsh Reality (the brother of the more infamous Chaos).