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I recently read an article on how DNA barcoding was used to identify species present in health products.

I also read an article about how Real-Time PCR was used to identify meat species in meat products.

I'm curious as to why one method is used over another. I know that DNA barcoding uses mitochondrial DNA to detect species, and Real-Time PCR uses species-specific primers to detect species.

Am I correct in thinking that real-time PCR cannot identify unknown species, but can tell you if the DNA matches a specific species you're looking for? For example, if I test for E. zebra but find something else, I cannot identify that unknown species and more testing is required?

Whereas in DNA barcoding, all I do is match the results against a huge list of known species in a database, which means I can identify unknown species without providing any prior knowledge?

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  • $\begingroup$ PCR cannot identify species - this is usually done by sequencing. The only way to do so (for known species only) is to use species specific primers which either give you amplification of DNA or not. So can make a relatively simple yes or no decision on the presence of the species, but you cannot go further beyond this. $\endgroup$ – Chris Feb 12 '15 at 20:55
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You've done a pretty decent job of answering your own question, but there are a few things that can be elaborated on.

The general convention is to use the mitochondrial Cytochrome C Oxidase 1 (COI) gene for barcoding animals and chloroplast genes (rbcL, matK, and trnH-psbA) for plants. The three biggest reasons for selecting these genes are 1) their ubiquity; 2) the presence of many copies per cell, so it's easier to PCR amplify the sequences; and 3) mitochondrial and plastid DNA has a much higher mutation rate than nuclear DNA, making it possible to uniquely barcode very closely related organisms. This method is incredibly sensitive, reliable, and easy. The original DNA barcoding publication can be found at doi: 10.1098/rspb.2002.2218

Thanks to the efforts of consortia like CBOL, BOLD and iBOL, there are now many millions of reference sequences databased, covering pretty much any multicellular organism you are ever likely to encounter (assuming you don't work on a deep-seq sub or something).

As you say in your post, there are significant limitations to using qPCR to identify species. You have to know beforehand what it is you are looking for, and you are left with a simple yes-no. This is not to say there is no place at all for qPCR in the species identification game, however. The method is very fast, and in cases where you are only interested in detecting a single species or small number of species, it's much more convenient than getting the DNA sequenced (for example, during quality control in a meat processing plant, doi: 10.1080/02652030701584041).

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DNA Barcoding is a method or a protocol which, as you have already mentioned, uses genetic markers to identify species. The barcodes can be "scanned" using PCR.

Now Real-Time PCR is just a quantitative version of PCR. You don't need that to look for qualitative aspects. However in a mixed sample you may be able to calculate percentage constitution of the sample by each species, using Real-Time PCR.

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