Wednesday, August 29, 2012

High resolution melt

Shortly after the heated discussions about DNA Barcoding (Does it work? Is it science?...) abated people started to think about ways to apply it to existing challenges. Two parameters played a big role - cost and speed. Although prices for sequencing dropped over the last years a sequencing platform of any kind still represents quite an investment for a regular research lab, let alone the operating costs. The time it takes to obtain a sequence from a sample can be very short but this highly depends on equipment and workflows. Again, a small lab at a university usually doesn't provide results within a few hours. I am sure that readers with practical lab experience will also assent that it isn't easy to establish a new sequencing protocol in a lab and that it takes a while to have it run smoothly. 

So, what do you do when you need fast, robust and reliable identifications of a handful of species that are not easy to distinguish based on morphology? Ah yes, it needs to be cheap as well.

Elaine Fitzcharles a PhD student at the Scottish Oceans Institute, University of St Andrews is the most recent proponent of a method called High Resolution Melt (HRM). She was looking at a group of Antarctic fish, called Macrourus or rattails. These fish are the most common bycatch species in the toothfish industry and represent a very important prey item of toothfish. They were traditionally thought to consist of three species in the Southern Ocean: M. carinatus, M. holotrachys and M. whitsoni but a study using DNA Barcoding  found two morphotypes of M. whitsoni which differed from each other in their COI sequence, to the extent that they were considered to represent a fourth species. All of them are morphologically very similar and their taxonomic status has been confused, until recently, in part because of a paucity of comparative material. Some characters show overlap, and identification of species had been based on relatively few specimens, using a combination of characters including geographic and depth distributions. An ideal test case for any genetic technique and based on the results of earlier DNA Barcoding work Elaine Fitzcharles was able to develop a HRM protocol that represents a quick and cost effective method of genetic screening and an alternative to DNA sequencing between the four also genetically very similar species.

1.7 Million DNA Barcodes for some 160,000 species have been assembled so far. The study ends with the following paragraph and there isn't much I could add to it.

"HRM analysis can utilise this barcoding resource for primer design and provides a quick, efficient, low cost alternative to DNA sequencing for species identification screening that could increase sampling opportunities and possibilities. This has the potential to greatly expand the scope of research available for both conservation genetics and fisheries management. The simplicity of the technology required and the technique opens up the possibility of routine genetic screening at remote locations such as research stations and onboard ships."

Macrourus whitsoni (source NIWA)

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