title: An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome.
abstract: 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 approximately 77% and P. vivax is approximately 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School and National Health Laboratory Service, York Road, Parktown, 2193, South Africa. durandp@pathology.wits.ac.za
authors.forename: Pierre M
authors.initials: PM
authors.lastname: Durand
authors.forename: Andries J
authors.initials: AJ
authors.lastname: Oelofse
authors.forename: Theresa L
authors.initials: TL
authors.lastname: Coetzer
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D014644:Genetic Variation; D018503:Genome, Protozoan / Q000235:genetics*; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010961:Plasmodium / Q000235:genetics*; D010963:Plasmodium falciparum / Q000235:genetics; D010966:Plasmodium vivax / Q000235:genetics; D010967:Plasmodium yoelii / Q000235:genetics; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity
chemical_list: D012194:RNA-Directed DNA Polymerase