Barcoding

Barcoding uses  short sequence of DNA from a standardized section of the gene, in animals not really in plants.

In 2003, Paul Hebert, researcher at the University of Guelph in Ontario, Canada, proposed “DNA barcoding” as a way to identify species. Barcoding uses a very short genetic sequence from a standard part of the genome the way a supermarket scanner distinguishes products using the black stripes of the Universal Product Code (UPC). Two items may look very similar to the untrained eye, but in both cases the barcodes are distinct.

The gene region that is being used for almost all animal groups, a 648 base-pair region in the mitochondrial cytochrome c oxidase 1 gene ("CO1"), is proving highly effective in identifying birds, butterflies, fish, flies and many other animal groups. The advantage of using COI is that it is short enough to be sequenced quickly and cheaply yet long enough to identify variations among species.

The COI barcode is not effective for identifying plants because it evolves too slowly, but two gene regions in the chloroplast, matK and rbcL, have been approved as the barcode regions for land plants.

In the laboratory, technicians use a tiny piece of tissue from the specimen to extract its DNA. The barcode region is isolated, replicated using a process called PCR amplification and then sequenced. The sequence is represented by a series of letters CATG representing the nucleic acids - cytosine, adenine, thymine and guanine.

So if you wrote down the barcode sequence of an Arctic warbler (Phylloscopus borealis), for example, it would look like this:

CCTATACCTAATCTTCGGAGCATGAGCGGGCATGGTAGGC....

And it's image looks like this

What has been termed DNA barcoding, is a new strategy for identifying species that has been rapidly spreading throughout all fields of biology, ecology, and conservation.  The process is, theoretically, pretty simple.  It relies on three basic assumptions about genetics: (1) there are certain genes that exist in the DNA of all animals; (2) the DNA code of these genes varies between organisms; (3) the DNA code of these genes is more different between two different species than between two individuals of same species (in other words, the difference is greater between a bullfrog and a toad than between two bullfrogs).  If all three of these requirements are met, then we can build a unique “barcode” for every animal, much like a store has a unique barcode of vertical lines that identifies each product sold.

Scientists have found a gene that satisfies these three requirements.  It is a gene found within the mitochondria of cells called cytochrome oxidase subunit or more commonly abbreviated as cox1 or COI.

So how does it work?  The first step is to build a database of known organisms, organisms that have been identified by more traditional methods.  Then, take a sample of DNA from the organism you want to identify.  Then sequence the COI gene.  You can then cross reference the sequence you obtained against a database of known organisms.  If you get a match, then you know what species you have.  If you don’t get a match, then much like a criminal forensics team, you have more research to do and evidence to gather.

Creating a lineage barcode  see cracking the code of... oppposite

With the advent of CRISPR gene editing technology and next generation sequencing, the idea that had been nagging at Shendure for years finally seemed possible to implement. Working in zebrafish and together with his collaborator Alexander Schier at Harvard University, his team inserted a “barcode” sequence of DNA into the genome of a fertilized zygote, and then also injected the Cas9 protein and guide RNAs that would allow the cell to generate unique mutations with every cell division. Having set the machine in motion, they stepped back and observed as the barcode they inserted into just one cell became more and more differentiated with each new generation of daughter cells.

When it came time to analyze the results, Shendure’s team used the patterns in the mature cells’ barcodes to trace back the origins of each cell. “If we see a change in the barcode that’s consistent across many of the cells, we can assume that the mutation took place earlier in the organism’s development, while rarer mutations probably happened later,” he explains. “We can use that information to learn not just about the progenitors of any given cell, but about the relationships between mature cells.”

Barcoding

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