Comparative description of macronuclear electrophoretic karyotypes of Paramecium primaurelia and Paramecium novaurelia sibling species

The macronuclear genomes of two sibling species belonging to the Paramecium aurelia complex, P. primaurelia and P. novaurelia, were analyzed by pulsed-field gel electrophoresis (PFGE). Their electrophoretic karyotypes showed a continuous spectrum of different-sized DNA molecules with a species-specific pattern of banding, which was reproducible and did not change with strain senescence. Thus, P. aurelia macronuclear PFGE profiles could be described by an approach analogous to that used for the description of metaphase chromosome banding patterns. First, well-identifiable regions (size fractions) of the PFGE profile, which could be seen at any resolution, are determined. Then, bands of the second order of resolution (subfractions) can be detected in some regions. The blocks of the first and second order can be utilized as internal markers of the PFGE profile, as they allow for a precise comparison of different PFGE profiles. Such comparative analysis has demonstrated some marked differences in organization of the macronuclear genomes of P. primaurelia and P. novaurelia and a low level of intraspecies polymorphism. It is worth noting that the P. novaurelia strain isolated in the United States was different from all other analyzed P. novaurelia strains of European origin. The nature of banding of the P. aurelia PFGE profiles is discussed. The revealed high order and stability of the macronuclear genome organization makes it possible to search for new approaches to studying the mechanisms of this nontrivial genome formation and maintenance. Further PFGE analysis of the macronuclear genomes of the other Paramecium species in relation with the Paramecium phylogeny may provide insights into directions of evolution of the macronuclear genome in Ciliata.