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I have to check if some genes are amplified with bioinformatics tools, but, in order to do it, I need to know what this means from a biological point of view.

It seems not so difficult to understand, in fact the definition from NIH is simply the following:

Gene amplification is an increase in the number of copies of a gene sequence. Cancer cells sometimes produce multiple copies of genes in response to signals from other cells or their environment. The term also can refer to polymerase chain reaction (PCR), a laboratory technique that is used by scientists to amplify gene sequences in a test tube.

So my question is: if I have the complete DNA sequence of the organism's genome that I am studying (like this), that belongs to Archaea domain, what I should do to check for gene amplification is to see if the sequence of the gene (that I suspect that it is amplified) is repeated more times ?

I thank you in advance.

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    $\begingroup$ Could you clarify a few points to produce a focused question on the biology rather than the bioinformatics. (Of course a question on the bioinformatics is acceptable, but one at a time is how this site works. The two are separate questions.) When you say "how gene amplification is present in the genome" what do you mean? Do you mean how does it occur mechanistically, or what function can it serve? And it would be good to say whether you are interested in prokaryotes (as it appears) or eukaryotes, because the situations are rather different in the two cases. $\endgroup$
    – David
    Jun 8 at 17:11
  • $\begingroup$ @David ok I will correct it but with the "how gene amplification is present in the genome" I mean how the genome DNA sequence is after gene amplification... so I am not interested in how it occurs mechanistically or what function it can serve (unless it is needed to understand what I want to know)... so in the sequence that I linked, should I simply find the sequence of a gene more times if it has been amplified ? $\endgroup$
    – Manuela
    Jun 8 at 17:21
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    $\begingroup$ I appreciate the linguistic usage problems with the English word “how” for non-native speakers (French, German and Italian, rather than Spanish which I assume is not too different). The usage you employed seems logical (= “how are amplified genes arranged/disposed in the genome?”) but is never employed. I would perhaps write something like “What is the typical arrangement of amplified genes in bacteria, especially those features that one might regard as indicative (or signatures) of amplification?”. It is not my particular area or I would answer. $\endgroup$
    – David
    Jun 8 at 18:13
  • $\begingroup$ Thank you very much @David for the suggestions $\endgroup$
    – Manuela
    Jun 8 at 19:15
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You ask "so in the sequence that I linked, should I simply find the sequence of a gene more times if it has been amplified ?"

Yes. There are many ways, both natural and artificial, to end up with more copies of a certain gene or genes without a proportional increase in copies of the other genes in the cell. Thus, there is no generally expected arrangement of the amplified genes.

One aspect to think about is the criteria for determining whether two given genes are copies of the same gene or are two distinct genes.

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  • $\begingroup$ Thank you for your answer but I do not understand when you say One aspect to think about is the criteria for determining whether two given genes are copies of the same gene or are two distinct genes, because, if they have the same sequence, they should be certainly the same, right ? $\endgroup$
    – Manuela
    Jun 9 at 7:58
  • $\begingroup$ I added a new post focused only on the second question, so if you want to have a look here biology.stackexchange.com/questions/101133/… you can understand better what I meant . Sorry for these jumpings :) $\endgroup$
    – Manuela
    Jun 9 at 9:19
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    $\begingroup$ @Manuela Re: " if they have the same sequence, they should be certainly the same, right ?" Right, but many (most maybe) processes that produce gene amplification will result in mutations in one or more copies, either immediately or over time. For example, a duplicated segment of chromosome may initially have the same genes, but absent strong selection those will diverge over time. Maybe the copies still function the same, maybe they don't. $\endgroup$
    – Armand
    Jun 9 at 12:25
  • $\begingroup$ Thank you ! Things are much more complicated than I thought. Is there a criteria to enstablish if they are copies of the same gene, as you mentioned in the answer ? And, moreover, can you suggest some books or material that explains with more details what you said to me in the answer (so about the fact that we should see in the genome sequence different copies of the gene duplicated) ? $\endgroup$
    – Manuela
    Jun 9 at 12:35
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    $\begingroup$ @Manuela My perspective is gene duplication in mammals over evolutionary time, so I would give an example of something like "Evolution of olfactory receptor genes in the human genome" doi: 10.1073/pnas.1635157100 and the follow-on work. Your perspective seems to be much more short-term oriented (and not eukaryotic!), so something like "Bacterial gene amplification: implications for the evolution of antibiotic resistance" Nat Rev Microbiol. 2009 Aug;7(8):578-88. doi: 10.1038/nrmicro2174 might be more to your interest. $\endgroup$
    – Armand
    Jun 9 at 12:59

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