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We can get many DNA sequences at NCBI websites for free. Is there any websites that provide the DNA sequences of food especially meat, for free?

When I read papers regarding food authentication, they only stated the exact DNA sequence for the primers only, not the DNA sequence of their food samples. Why primers? Is it because scientists from the same field can guess what the sample's sequence will be?

Alternatively, if there's no site that shares the DNA sequence of food samples, is there any other place where I can get DNA sequence of mixed species or mutation? For free.

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    $\begingroup$ They use primers because the DNA of an animal is enormous and they only want to amplify a certain part of the DNA that can help them distinguish one species from another. As far as I am aware, for food fraud purposes DNA sequencing is not routinely done (just because it is quite a resource-intensive process), instead simple electrophoresis is used to separate fragment size. So the sequence itself doesn't matter - it's the fragment length that is used to distinguish species and detect meat/dairy fraud. However I'm sure sequencing will be used more commonly for this purpose in the future. $\endgroup$ – Harry Vervet Jan 29 '16 at 5:18
  • $\begingroup$ Thank you for your valuable explanation. Just to clarify that I understand the big picture : first, use primer just for amplification - then amplify (PCR) - then use electrophoresis - then bands appear - results: band with length A belongs to species X, if length B then species Y, and so on. If wrong please correct me. So they don't need compare the amplification product with any database of species' DNA sequence? That seems nice..or maybe I dont understand its drawback. Why do you said sequencing will be common for food fraud in the future? I'm interested in knowing that. $\endgroup$ – kate Jan 29 '16 at 6:14
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    $\begingroup$ Yes, you can compare the length of the PCR product to a known database of species, presumably knowing what species to expect. Sequencing is still a relatively expensive and intensive technique, but as it becomes cheaper and easier it will probably become more popular since it's more sensitive than electrophoresis and gives you more information. There are other genetic technologies used in food fraud as well. I don't have time to write this up as an answer now, but will do so later and add more details if nobody beats me to it. $\endgroup$ – Harry Vervet Jan 29 '16 at 6:31
  • $\begingroup$ Thank you so much! In my opinion i've read many papers and some books on dna-based food authentication and dna sequencing, but without basic knowledge on biotech (only high school bio). i got confused thus mixed them up..thanks for clearing me up. other than drawbacks, i am interested in how PCR product is compared with the database part also.. thank you for sharing your knowledge even in your busiest time. $\endgroup$ – kate Jan 29 '16 at 8:58
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I am not aware of any websites that provide full DNA sequences for food products specifically. In the context of your question, by "food samples" I am assuming you are chiefly referring to meat, fish, and dairy products (the headline-making categories of food fraud), although similar principles are applied to plant products, oils, rice, and other natural products.

PCR

There are a wide variety of genetic techniques used to detect food fraud or adulteration. These techniques do not look at the entire genome of the animal or plant from which it is derived – that would be extremely expensive and unnecessary. Instead, scientists look at particular parts of the genome that they know will likely help them distinguish one species from another.

This is where the primers come in. DNA primers are short segments of DNA that are used to initiate replication of segment of DNA, and is the vital component of PCR that determines which part of the genome will be amplified. Once the PCR product is amplified, it can be analysed by a variety of techniques. For instance, if the PCR products of various species are known, they can simply be run on gel electrophoresis which separates the DNA products by size. Thus if a band of an unexpected size appears on the gel you know there has been some contamination. There are also more automated methods of detecting fragment size via electrophoresis.

Examples of where these techniques has been used has been to detect:

From the López-Calleja study on mozzarella, one of the gels looked like this:

enter image description here

The PCR was run to detect cow's milk in buffalo cheese. Lane 1 corresponds to 100% cow's milk (it is a very bright band), lane 2 is 10% cow's milk, ranging down to lane 6 which has 0.1% cow's milk (a very faint band), and lane 7 is the pure buffalo cheese which shows no band. Therefore, this assay could be useful to rule out contamination with cow's milk.

Real-time PCR

Running gels is a somewhat old-fashioned way of doing things, and there are better ways to make use of PCR technologies on a larger scale. Real-time PCR is the technique now routinely done to detect food fraud. This is a variant of PCR, which (as the name suggests) allows one to quickly see which PCR products are being produced, in what quantity, and there is no need to run a gel.

For example, real-time PCR has been used to detect:

An example of what the read-out from the real-time PCR is given below. This example is from the Ali study on beef burger adulteration. The letter A was 100% adulterated (i.e. contained 100% pork instead of beef), letter B contained 10% pork, and so-on to E which contained 0.01% pork. F had no pork. The more pork contamination there was, the sooner on the plot (in PCR cycles) the contaminant reached detectable levels:

enter image description here

About the sequence

As you will see from reading about these techniques, it is not so much the sequence itself which is important – it is fragment size or other properties of the region analysed by PCR that is most practically useful. Sometimes the PCR product may be sequenced for comparison purposes, although I do not believe this is done as a routine screening for food fraud.

Keep in mind that PCR is just one of a number of genetic techniques used in food safety. For example, DNA barcoding and SNPs are also useful techniques that are used in this field. The technology is constantly improving and evolving and no doubt more refined and efficient methods are being developed to detect food fraud.

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  • $\begingroup$ This is much better than what I read by myself. Having a great teacher really makes differences. Particularly on how the fraud is detected by each technique. Thank you very much! $\endgroup$ – kate Jan 30 '16 at 4:57

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