BMC Genomics Research article An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome Pierre M Durand*1, Andries J Oelofse2 and Theresa L Coetzer1 BioMed Central Open Access Address: 1Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School and National Health Laboratory Service, York Road, Parktown, 2193, South Africa and 2Wits Bioinformatics, University Corner building, University of the Witwatersrand, Johannesburg, 2017, South Africa Email: Pierre M Durand* - durandp@pathology.wits.ac.za; Andries J Oelofse - ajoelofse@bioinf.wits.ac.za; Theresa L Coetzer - theresa.coetzer@nhls.ac.za * Corresponding author Published: 04 November 2006 BMC Genomics 2006, 7:282 doi:10.1186/1471-2164-7-282 This article is available from: http://www.biomedcentral.com/1471-2164/7/282 Received: 08 August 2006 Accepted: 04 November 2006 © 2006 Durand et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 ~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. Background Mobile genetic elements (MGEs) play a fundamental role as drivers of genome evolution, shaping both genes and genomes and often constitute a large fraction of the genome (for a review of mobile elements and genome evolution see [1,2]). The mutagenic effects of MGE behav- iour are well documented and include a spectrum, from point mutations to whole genome restructuring. In addi- tion, MGEs have occasionally become "domesticated" and evolved to fulfill essential functions in genome Page 1 of 10 (page number not for citation purposes)