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Suppose there is a GeneBank DNA sequence listed that produces a specific enzyme in a specific species of plant. e.g. A terpene Synthase.

Now if someone samples various trees of the same species would one expect to get the exact same sequence each time? Or is a certain amount of variation expected from tree to tree?

The drift behind my question is: Obviously not all tress of the same species are exactly identical in phenotype. So are the causative factors seen in sequence variations of various enzymes etc.? Or can we expect the various samples to have exactly identical amino acid / DNA sequences for particular genes / enzymes.

e.g. e.g. Take this specific sequence: http://www.uniprot.org/uniprot/E3W202 If I sample from various trees of this same species and sequence this particular gene how much variation should I expect? Or would they be almost 100% identical?

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  • $\begingroup$ It may or may not vary much. Unless you have additional information, it would be hard to tell. Try looking at conservation across different species. That may give some clue. $\endgroup$ – WYSIWYG Jun 21 '16 at 18:46
  • $\begingroup$ Is there a correlation between conservation across different species & within species variation? $\endgroup$ – curious_cat Jun 22 '16 at 3:22
  • $\begingroup$ Can't say for sure and I have not come across any study like that but conservation across different species can indicate that variation in the sequence may probably reduce fitness and same may apply for "within species". $\endgroup$ – WYSIWYG Jun 22 '16 at 4:29
  • $\begingroup$ Thanks @WYSIWYG I am surprised that there is no information of how much of a within species variation there is in enzyme sequence. I am having a hard time getting this info. too. $\endgroup$ – curious_cat Jun 22 '16 at 4:34
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    $\begingroup$ @curious_cat: I just stumbled across this: sciencedirect.com/science/article/pii/S2213596014001238. There it was found some conserved genes between humans and fruit flies in which there is substantial sequence variation within the respective species. $\endgroup$ – AlexDeLarge Jun 22 '16 at 12:11
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Your question is quite vague so I can only give you a vague answer saying what I would expect given only the information of your question.

The vagueness mainly comes from the huge amount of functional sequences in the genome, particularly also in enzyme-coding genes, each being more or less conserved. You say

I am surprised that there is no information of how much of a within species variation there is in enzyme sequence. I am having a hard time getting this info. too.

I would say that there is no feasible way of studying this question. You will find different selective constraints on every single enzyme and breaking this down to DNA this means that every single locus can be target of different selective pressures. And even if you figured out how to answer that question comprehensively for a given species (which probably will not happen), generalising it to every single species in every ecological niche, with every possible population history and so on is close to impossible. That is why one studies sequence diversity/conservation in model organisms and mostly on a per-gene basis.

In general, without knowing any background of a species and enzyme, I would however expect two things when looking at molecular variation between individuals of that species. These are merely based on general evolutionary principles and the nature of the genetic code. Keep in mind that these are trends, meaning that many genes will match these expectations but some definitely will not due to lineage-specific evolution.

First, I would expect generally high levels of amino acid conservation (but not always identity) especially in functional enzymes of core pathways. However, this depends on the function of the gene product. If the gene is a target of balancing selection, which maintains genetic variation within a population, there can also be considerable amino acid variation.

Second, there will generally be higher levels of DNA variation because of mutations with little or no fitness effect (synonymous variation or intronic variation which tends to have lower selective pressure).

To relate this to your last question: even though I would always expect a general amount of variation, even in the amino acid sequence of core enzymes, this variation will probably not be the main reason why you see different phenotypes. Phenotypic plasticity - the differential response of a given genotype to a given environment - is often stronger in plants than in animals as plants are stationary organisms. This plasticity will probably be the main cause of striking phenotypic differences between individuals.

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  • $\begingroup$ Sorry about the vagueness. Can you comment on what parts I have left ambiguous so I can improve my question? e.g. Take this specific sequence: uniprot.org/uniprot/E3W202 If I sample from various trees of this same species and sequence this particular gene how much variation should I expect? Or would they be almost 100% identical? $\endgroup$ – curious_cat Jun 21 '16 at 14:53
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    $\begingroup$ I did not mean your question was hard to understand. The vagueness comes from that there is no information on the species and the species' population history. This strongly affects the expectations of variation within a species. My answer are just some vague pointers what to think about. I will later think about if I have something more to add. :) $\endgroup$ – AlexDeLarge Jun 21 '16 at 15:15
  • $\begingroup$ Thanks! I added some info. about the enzyme as well as the species so maybe that helps you formulate a more concrete answer? $\endgroup$ – curious_cat Jun 21 '16 at 15:21
  • $\begingroup$ To expand more: I know that there are homologous enzymes across species e.g. The enzyme or gene coding for (say) Squalene from its precursor will look similar with some regions changed. And BLAST etc. identifies this. What I am wondering here is within the same species but in different samples, how much variation is there typically in the sequence of the same enzyme. $\endgroup$ – curious_cat Jun 21 '16 at 15:23
  • $\begingroup$ @curious_cat: I added some further comments on the problem. In my view this is not really a biological problem but rather a philosophical one. $\endgroup$ – AlexDeLarge Jun 22 '16 at 10:08

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