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Background  Malaria parasites of the genus  Plasmodium  possess large hyper-variable families of antigen-encoding genes. These are often variantly-expressed and are major virulence factors for immune evasion and the maintenance of chronic infections. Recombination and diversification of these gene families occurs readily, and may be promoted by G-quadruplex (G4) DNA motifs within and close to the variant genes. G4s have been shown to cause replication fork stalling, DNA breakage and recombination in model systems, but these motifs remain largely unstudied in  Plasmodium .    Results  We examined the nature and distribution of putative G4-forming sequences in multiple  Plasmodium  genomes, finding that their co-distribution with variant gene families is conserved across different  Plasmodium  species that have different types of variant gene families. In  P. falciparum , where a large set of recombination events that occurred over time in cultured parasites has been mapped, we found a strong spatial association between these recombination events and putative G4-forming sequences. Finally, we searched  Plasmodium  genomes for the three classes of helicase that can unwind G4s:  Plasmodium spp.  have no identifiable homologue of the highly efficient G4 helicase PIF1, but they do encode two putative RecQ helicases and one homologue of the RAD3-family helicase FANCJ.    Conclusions  Our analyses, conducted at the whole-genome level in multiple species of  Plasmodium , support the concept that G4s are likely to be involved in recombination and diversification of antigen-encoding gene families in this important protozoan pathogen.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3183-3) contains supplementary material, which is available to authorized users.

Recombination events among virulence genes in malaria parasites are associated with G-quadruplex-forming DNA motifs