What is the nature of inserts between the forward and reverse priming sites? What will be the properties?
Hi Binoy,
During the evolution of the SSR loci repeat numbers change to generate multi alleles in a single locus. but I do not think that we can simulate or model SSR evolution because of random and complex evolutionary nature of the marker.
Hi Binoy,
Basically, when we amplify a SSR loci, the repeats itself represent one part of the sequence which is amplified: let's say from 30 to 60%, and then extra fragments can be seen as a kind of spacer to the priming site which has the right properties for the amplification. The spacer can be any sequence but are usually not SSR themselves. As a consequence when we sequence an amplified SSR locus, we have the lateral fragments (genes, intergenic regions etc...), and then the SSR repeats.
About SSR evolution, different models are used in order to model SSR evolution, especially for population historical inferences such as with ABC analyses. The first models proposed were the stepwise mutation model (SMM) , and Estoup et al. 2002 Mol Ecol 11 ,1591 proposed the Generalized Stepwise mutation model, which takes into account different steps, such it is used for ABC simulation in DIYABC software. Last differences in the sizes of SSR alleles can be taken into account in genetic distances such as delmu2 distance (Goldstein 1995) which assumes SMM or Bruvo's distance. (Bruvo, 2004 Mol Ecol 13,2101).
Good luck. Cheers.
Jean-Luc
Hey! My question do you want to sequence the SSR product? If yes its fine, I answer your question. Why the question of evolution come here, amazing and interesting answers!!
The nature is the same in general terms, but its easier to get sequences and more accurate.
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