|Some examples of the use of 'universal'' primers|
In this genus, a region close to the ycf9 genes contained a number of species- or clone-specific polymorphisms, which could be clarified by simple restriction mapping (picture). On the basis of these results, simple tests for rapid species identification could be developed (Krystufek 2001).
Cherry restriction maps (Prunus avium L.; Heinze, unpublished)
In this species, many small indels occur. Some of the seem to be clustered in the trnR-atpA region. Restriction mapping of overlapping PCR fragments revealed location of the indels and allowed greater resolution for haplotypes.
Denaturing HPLC analysis of chloroplast DNA variation
Heteroduplex analysis was conducted with a VARIAN gradient HPLC system. Heteroduplices partially melt at critical temperature and give an indicative pattern in this system. Point mutations in fragments up to 700 bp can be detected. The system is especially suitable for screening large number of samples.
Mutation hotspots ?
Our preliminary data reveal that the junction of the inverted repeat A and the large single copy region is polymorphic within many species. Several authors have found polymorphisms in ths region (Jackson et al. 1999). Other regions are sometimes highly polymorphic, but only for specific taxa (e.g., the ycf9 region in Populus).