I try to make a low-level phylogeny based on highly variable cp-spacers. But after PCR, cloning and sequencing I obtained quite different products from 1 organism. It's looks like quite strange, because in this case cpDNA is maternally inherited and I expect to obtain one haplotype. The differences can't be explained by polymerase errors.
It can bear a copy of cpDNA in another cell compartment (e.g. via horizontal gene transfer). An example in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598846/
Dear Nina,
did you find two types of cpDNA in one plant or not? Because in your article it seems to be different plants in analysis
Dear Nina,
Thank you very much for clarification. It's not surprising to have different cp haplotypes for different plants. But in my case I found different haplotypes in the same plant and this fact looks quite surprising.
Luis (first answer) already provided the most likely answer to the question - copies of cp DNA in the nuclear (nc) genome. that is a frequently found thing. My suggestion is to check all your taxa for muliple PCR products. The expectation is that there would be hardly or no differences in the cp copies but multiple in the nc copies (including loss of function mutations) in closely related species - depending on the time when the horizontal transfer took place. It could be fun to include more and more distantly related taxa in order to see when you stop picking up the nc copies.
if the plant you study is sexually reproducing it may have received cp DNA from its two parents! it is a rare event but such facts have been described in the plant litterature, search for the father :) ; some recombinations are also possible and may be the plant you study has an original cp DNA structure which produces intramolecular recombination and different haplotypes from the same genome as has been described in plant mt DNA
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