Dear Binaya, although it is a bit old, but a nice summary of  the question worth to read.

hi, Binaya

First you must know what you want? Polymorphism in size or sequence, in both cases it is interesting even in the presence of duplicate gene. Shall put the problem may be in the case of a PCR-RFLP.

To add a little detail, I am talking about sequences data and where PCR amplification and sequencing is successful. Could there be variations associated with different inheritance patterns of mitochondrial and nuclear copies (if present) or may be the two copies could have different substitution rates?  PCR reaction may pick any fragment from the total DNA if primers work for both. 

Hi Binaya

It shouldn't be difficult to sort out both sequences (unless duplication: i.e., the pseudogene, has appeared very recently). In the latter case, you might want to use a different (pseudo)gene.

Indeed, substitution rates are different in the two cases. Just consider that purifying selection will act on the gene but not on the pseudogene.

Regarding your first statement: "Plant mitochondrial pseudogenes tend to accumulate neutral mutations....", i would say that all mutations within pseudogenes are neutral (unless a very rare gain of function mutation will occur). Therefore, I would rather say "Plant mitochondrial pseudogenes tend to accumulate mutations..."..

Hope this helps

Pablo

the rate of mutation at the nuclear level is more important than at the mtDNA causes crosing over. IN THIS CASE YOU CAN FIND DIFFERENT SEQUENCES

Thanks for the responses so far. Could you make your second answer little clear Dr. Gaouar?

Also, I think use of specific primers helps sort out pseudogene sequences from duplicated sequence. I have read in places that the duplicated copies are usually shorter than the original mitochondrial version. This difference may also help figure out which copy was actually amplified. I would appreciate any responses.  

Hi Binaya

Pseudogenes are duplicated sequences. Because the function of the gene is ensured by the original copy, the pseudogene (duplicated sequence) can evolve much faster. This usually leads to loss of function, accumulation of otherwise lethal mutations, etc. (e.g., higher mutation rates because there is no functional constraints)

Mitochondrial sequences can recombine, thus making possible to have a higher apparent mutation rate. But nuclear sequences can recombine too (so, I do not understand last Semir comment either).

It is dubious that you amplify the gene and the pseudogene at the same time (with the same primers). However, if this were the case, both types should be easily identified by CLUSTAL analysis.

There is several examples of this with rDNA, which is a mulitcopy segment.

Pablo

Thanks Dr. Goicoechea. This discussion helps. Can we also think of a situation where a gene becomes pseudogene because its function is taken over/replaced completely by some other gene so that the pseudogene in question is of no use e.g. some ribosomal protein genes but the pseudogene is still not yet removed from the genome? In this case, the functional copy does not exist anywhere. Thanks.

Indeed, you could think of very complicated situations. However, if the function is taken over/replaced by some other gene, there you have the functional copy. But, please, keep in mind this would be a very rare situation.

The normal process would be: 1) duplication (then you have two functional copies); 2) one of the copies accumulates mutations because the function can be maintained by the other copy; 3) the copy that has accumulated mutations becomes a pseudogene with no function.

Pablo

Dear Binaya, although it is a bit old, but a nice summary of  the question worth to read.

Thank you Dr. Goicoechea for valuable comments and Dr. Csuzdi for the paper. 

Hmm.. Since when have mitochondrial genes which are only passed on through the mother subject to recombination? How does that work?

Pseudogene is not synonymous with gene duplication. Families of perfectly functional genes arise from gene duplications. A duplicated gene is not a pseudogene unless it loses function and coding capabilities through uncorrected mutation.

Recombination of heteroplasmic mitochondrial genomes has been found is some plant species and paternal leakage is believed to occur, particularly in gynodioecious plants.  

Regarding pseudogenes I was also thinking about those pseudogenes that are not duplicated anywhere. They became non-functional because their function is no longer needed or some other existing genes can do that function.    

What I know of plant mitochondrial genomes is very little. Thanks for the clarification.

Hi Patrice

Which group/species are you thinking of? Most species will pass mitochondrial DNA through both parents....

I have not state pseudogene=gene duplication. However, most pseudogenes will occur through gene duplication and loss of function of one of the copies. I agree some may occur because the function is no longer needed, or because some other existing genes can do that function, but these will be minority.

Although this is nuclear genome, just think about genome duplications that have occurred through plants evolution. Indeed, some of the duplicated genes might have gained another function, but most of the duplications will become pseudogenes.

Hope this helps.

Pablo

Because Pseudogenes are not subject to selective pressure or functional constraints and easily accumulate mutations in their sequence, they can be used as markers.