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Background  The  Plasmodium  genus of malaria parasites encodes several families of antigen-encoding genes. These genes tend to be hyper-variable, highly recombinogenic and variantly expressed. The best-characterized family is the  var  genes, exclusively found in the Laveranian subgenus of malaria parasites infecting humans and great apes.  Var  genes encode major virulence factors involved in immune evasion and the maintenance of chronic infections. In the human parasite  P. falciparum ,  var  gene recombination and diversification appear to be promoted by G-quadruplex (G4) DNA motifs, which are strongly associated with  var  genes in  P. falciparum . Here, we investigated how this association might have evolved across  Plasmodium  species – both Laverania and also more distantly related species which lack  var s but encode other, more ancient variant gene families.    Results  The association between  var  genes and G4-forming motifs was conserved across Laverania, spanning ~ 1 million years of evolutionary time, with suggestive evidence for evolution of the association occurring within this subgenus. In rodent malaria species, G4-forming motifs were somewhat associated with  pir  genes, but this was not conserved in the Laverania, nor did we find a strong association of these motifs with any gene family in a second outgroup of avian malaria parasites. Secondly, we compared two different G4 prediction algorithms in their performance on extremely A/T-rich  Plasmodium  genomes, and also compared these predictions with experimental data from G4-seq, a DNA sequencing method for identifying G4-forming motifs. We found a surprising lack of concordance between the two algorithms and also between the algorithms and G4-seq data.    Conclusions  G4-forming motifs are uniquely strongly associated with  Plasmodium var  genes, suggesting a particular role for G4s in recombination and diversification of these genes. Secondly, in the A/T-rich genomes of  Plasmodium  species, the choice of prediction algorithm may be particularly influential when studying G4s in these important protozoan pathogens.

Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites