Chromosome size polymorphisms in Plasmodium falciparum can involve deletions and are frequent in natural parasite populations.

A comparison of independent cultured isolates of Plasmodium falciparum revealed that while chromosome number was constant, the sizes of analogous chromosomes varied widely. We show here that chromosome size polymorphisms are not generated during differentiation of the asexual blood stages, as the molecular karyotype of a cloned parasite line is constant through this part of the life cycle. Experiments using whole P. falciparum chromosomes as hybridization probes to examine polymorphisms within two independent parasite populations indicate that the polymorphisms observed here are not the consequence of large-scale interchromosomal exchanges, and imply that deletions/duplications represent one mode of generating chromosome length polymorphisms. Although the deletions probably involve repetitive DNA, we show here that structural genes for P. falciparum antigens can also be lost. Furthermore, these dramatic size polymorphisms occur not only in cultured lines of P. falciparum, but with surprising frequency in natural malarial infections.