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Background  The completed genome sequences of the malaria parasites  P. falciparum ,  P. y. yoelii  and  P. vivax  have revealed some unusual features.  P. falciparum  contains the most AT rich genome sequenced so far – over 90% in some regions. In comparison,  P. y. yoelii  is ~77% and  P. vivax  is ~55% AT rich. The evolutionary reasons for these findings are unknown. Mobile genetic elements have a considerable impact on genome evolution but a thorough investigation of these elements in  Plasmodium  has not been undertaken. We therefore performed a comprehensive genome analysis of these elements and their derivatives in the three  Plasmodium  species.    Results  Whole genome analysis was performed using bioinformatic methods. Forty potential protein encoding sequences with features of transposable elements were identified in  P. vivax , eight in  P. y. yoelii  and only six in  P. falciparum . Further investigation of the six open reading frames in  P. falciparum  revealed that only one is potentially an active mobile genetic element. Most of the open reading frames identified in all three species are hypothetical proteins. Some represent annotated host proteins such as the putative telomerase reverse transcriptase genes in  P. y. yoelii  and  P. falciparum . One of the  P. vivax  open reading frames identified in this study demonstrates similarity to telomerase reverse transcriptase and we conclude it to be the orthologue of this gene.    Conclusion  There is a divergence in the frequencies of mobile genetic elements in the three  Plasmodium  species investigated. Despite the limitations of whole genome analytical methods, it is tempting to speculate that mobile genetic elements might have been a driving force behind the compositional bias of the  P. falciparum  genome.

bmc genomics

An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome