BMC Genomics 2006, 7:282 http://www.biomedcentral.com/1471-2164/7/282 Sequence data for the P. vivax genome was obtained with permission from The Institute for Genomic Research. Sequencing of the P. vivax project was accomplished with support from National Institute of Allergy and Infectious Diseases (NIAID), the US Department of Defense (DoD), and the Bur- roughs Wellcome Fund. References 1. Kazazian HH Jr: Mobile Elements: Drivers of Genome Evolu- tion. Science 2004, 303:1626-1632. 2. Kidwell MG, Lisch DR: Perspective: Transposable Elements, parasitic DNA, and Genome Evolution. Evolution 2000, 55:1-24. 3. Lin YJ, Seroude L, Benzer S: Extended life-span and stress resist- ance in the Drosophila mutant methuselah. Science 1998, 282:943-946. 4. Le Rouzic A, Capy P: The first steps of transposable elements invasion: parasitic strategy vs. genetic drift. Genetics 2005, 169:1033-1043. 5. Freitag M, Williams R, Kothe GO, Selker EU: A cytosine methyl- transferase homologue is essential for repeat-induced point mutation in Neurospora crassa. Proc Natl Acad Sci 2002, 99:8802-8807. 6. Luan DD, Korman MH, Jakubczak JL, Eickbush TH: Reverse tran- scription of R2Bm RNA is primed by a nick at the chromo- somal target site: a mechanism for non-LTR retrotransposition. Cell 1993, 72:595-605. 7. Belfort M, Perlman PS: Mechanisms of Intron Mobility. J Biol Chem 1995, 270:30237-30240. 8. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carl- ton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan M-S, Nene V, Shal- lom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DMA, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419:498-518. 9. Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermo- laeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cum- mings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cun- ningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ: Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 2002, 419:512-519. 10. Bottius E, Bakhsis N, Scherf A: Plasmodium falciparum Telomer- ase: De Novo Telomere Addition to Telomeric and Nonte- lomeric Sequences and Role in Chromosome Healing. Mol Cell Biol 1998, 18:919-925. 11. Rubiano CC, Wasserman M: Identification of the gene sequence of telomerase catalytic subunit in Plasmodium falciparum. Bio- medica 2005, 25:87-100. 12. Figueiredo LM, Rocha EPC, Mancio-Silva L, Prevost C, Hernandez- Verdun D, Scherf A: The unusually large Plasmodium telomer- ase reverse transcriptase localizes in a discrete compart- ment associated with the nucleolus. Nucleic Acids Res 2005, 33:1111-1122. 13. Dhar A, Gupta S, Sharma YD: Alu elements in a Plasmodium vivax antigen gene. FEBS Lett 1998, 423:193-197. 14. Figueiredo LM, Pirrit LA, Scherf A: Genomic organization and chromatin structure of Plasmodium falciparum chromosome ends. Mol Biochem Parasitol 2000, 106:169-174. 15. The European Bioinformatics Institute InterPro Database [http://www.ebi.ac.uk/interpro] 16. The Welcome Trust Sanger Institute Protein Family Data- base [http://www.sanger.ac.uk/Software/Pfam] 17. The Plasmodium Genome Resource Database [http:// www.plasmodb.org] 18. The Institute for Genome Research [http://www.tigr.org] 19. Altschul SF, Gish W, Miller W, Meyers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410. 20. Selker EU, Stevens JN: DNA methylation at asymmetric sites is associated with numerous transition mutations. Proc Natl Acad Sci USA 1985, 82:8114-8118. 21. Cambareri EB, Jensen BC, Schabtach E, Selker EU: Repeat-induced GC to AT mutations in Neurospora. Science 1989, 244:1571-1575. 22. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, Fit- zHugh W, Ma L-J, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Ped- ersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kin- sey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange- Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzen- berg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CPC, Glass L, Orbach MJ, Ber- glund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B: The genome sequence of the filamentous fungus Neurospora crassa. Nature 2003, 422:859-868. 23. Kuhlmann M, Borisova BE, Kaller M, Larsson P, Stach D, Na J, Eichinger L, Lyko F, Ambros V, Söderbom F, Hammann C, Nellen W: Silencing of retrotransposons in Dictyostelium by DNA meth- ylation and RNAi. Nucleic Acids Res 2005, 33:6405-6417. 24. Coates CJ, Jasinskiene N, Miyashiro L, James AA: Mariner transpo- sition and transformation of the yellow fever mosquito, Aedes aegypti. Proc Natl Acad Sci USA 1998, 95:3748-3751. 25. Eickbush TH: Telomerase and Retrotransposons: Which Came First? Science 1997, 277:911-912. 26. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D: Hidden Markov models in computational biology: applications to protein modeling. J Mol Biol 1994, 235:1501-1531. 27. Eddy SR: Hidden Markov Models. Curr Opin Struct Biol 1996, 6:361-365. 28. The HMMER Homepage [http://hmmer.janelia.org] 29. O' Reilly M, Teichmann SA, Rhodes D: Telomerases. Curr Opin Struct Biol 1999, 9:56-65. 30. Lingner J, Hughes TR, Shevchenko A, Mann M, Lundblad V, Cech TR: Reverse Transcriptase Motifs in the Catalytic Subunit of Tel- omerase. Science 1997, 276:561-567. 31. Xiong Y, Eickbush TH: Origin and evolution of retroelements based on their reverse transcriptase sequences. EMBO J 1990, 9:3353-3362. 32. The European Bioinformatics Institute [http://www.ebi.ac.uk/ emboss] 33. Thompson J, Higgins D, Gibson T: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 34. Carlton JM: The Plasmodium vivax genome sequencing project. Trends Parasitol 2003, 19:227-231. 35. The Human Genome Sequencing Center [http:// www.hgsc.bcm.tmc.edu] Publish with Bio Med Central and every scientist can read your work free of charge "BioMed Central will be the most significant development for disseminating the results of biomedical research in our lifetime." Sir Paul Nurse, Cancer Research UK Your research papers will be: available free of charge to the entire biomedical community peer reviewed and published immediately upon acceptance cited in PubMed and archived on PubMed Central yours — you keep the copyright Submit your manuscript here: http://www.biomedcentral.com/info/publishing_adv.asp BioMedcentral Page 10 of 10 (page number not for citation purposes)