Chromosome Research

, 19:787 | Cite as

Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes

  • Mateusz Janicki
  • Rebecca Rooke
  • Guojun Yang


A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out “junk” sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.


Transposable Element Bioinformatics Genomics Transposon 



Long interspersed nuclear element


Long terminal repeat


MITE analysis toolkit


Miniature inverted repeat transposable element


Mutator-like element


Short interspersed nuclear element


Transposable element


Transposable element simulator dynamics


Terminal inverted repeat


Target site duplication



This study was supported by National Sciences and Engineering Research Council (RGPIN371565 to G.Y.), Canadian Foundation for Innovation (24456 to G.Y.), Ontario Research Fund (24456 to G.Y.), and University of Toronto.


  1. Abrusán G, Grundmann N, DeMester L, Makalowski W (2009) TEclass—a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics 25(10):1329PubMedCrossRefGoogle Scholar
  2. Achaz G, Boyer F, Rocha E, Viari A, Coissac E (2006) Repseek, a tool to retrieve approximate repeats from large DNA sequences. Bioinformatics 23(1):119PubMedCrossRefGoogle Scholar
  3. Adams MD, Celniker SE, Holt RA et al (2000) The genome sequence of Drosophila melanogaster. Science 287(5461):2185–2195PubMedCrossRefGoogle Scholar
  4. Agarwal P, States DJ (1994) The repeat pattern toolkit (RPT): analyzing the structure and evolution of the C. elegans genome. Proc Int Conf Intell Syst Mol Biol 2:1–9 Google Scholar
  5. Arabidopsis-Genome-Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796–815CrossRefGoogle Scholar
  6. Aravind L (2000) The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases. Trends Biochem Sci 25(9):421–423PubMedCrossRefGoogle Scholar
  7. Arensburger P, Hice RH, Zhou L et al (2011) Phylogenetic and Functional Characterization of the hAT Transposon Superfamily. Genetics 188(1):45–57Google Scholar
  8. Babcock M, Pavlicek A, Spiteri E et al (2003) Shuffling of genes within low-copy repeats on 22qll (LCR22) by Alu-mediated recombination events during evolution. Genome Res 13(12):2519–2532PubMedCrossRefGoogle Scholar
  9. Babu MM, Iyer LM, Balaji S, Aravind L (2006) The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res 34(22):6505–6520PubMedCrossRefGoogle Scholar
  10. Babushok DV, Ostertag EM, Kazazian HH Jr (2007) Current topics in genome evolution: molecular mechanisms of new gene formation. Cell Mol Life Sci 64(5):542–554PubMedCrossRefGoogle Scholar
  11. Bailey JA, Liu G, Eichler EE (2003) An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet 73(4):823–834PubMedCrossRefGoogle Scholar
  12. Baldari CT, Amaldi F (1976) DNA reassociation kinetics in relation to genome size in four amphibian species. Chromosoma 59(1):13–22PubMedCrossRefGoogle Scholar
  13. Bao Z, Eddy SR (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 12(8):1269–1276PubMedCrossRefGoogle Scholar
  14. Bao WD, Jurka MG, Kapitonov VV, Jurka J (2009) New superfamilies of eukaryotic DNA transposons and their internal divisions. Mol Biol Evol 26(5):983–993PubMedCrossRefGoogle Scholar
  15. Barker RF, Thompson DV, Talbot DR, Swanson J, Bennetzen JL (1984) Nucleotide-sequence of the maize transposable element Mul. Nucleic Acids Res 12(15):5955–5967PubMedCrossRefGoogle Scholar
  16. Bartolome C, Maside X, Charlesworth B (2002) On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol Biol Evol 19(6):926–937PubMedGoogle Scholar
  17. Bartolome C, Bello X, Maside X (2009) Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes. Genome Biol 10(2):R22PubMedCrossRefGoogle Scholar
  18. Belancio V, Hedges D, Deininger P (2008) Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res 18(3):343PubMedCrossRefGoogle Scholar
  19. Belancio VP, Deininger PL, Roy-Engel AM (2009) LINE dancing in the human genome: transposable elements and disease. Genome Med 1(10):97PubMedCrossRefGoogle Scholar
  20. Belancio VP, Roy-Engel AM, Deininger PL (2010) All y'all need to know 'bout retroelements in cancer. Semin Cancer Biol 20(4):200–210PubMedCrossRefGoogle Scholar
  21. Bennett MD, Leitch IJ (2005) Genome size evolution in plants. In: Gregory TR (ed) The evolution of the genome. Elsvier, San Diego, pp 89–162CrossRefGoogle Scholar
  22. Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15(6):621–627PubMedCrossRefGoogle Scholar
  23. Bennetzen JL, Kellogg EA (1997) Do plants have a one-way ticket to genomic obesity? Plant Cell 9(9):1509–1514PubMedCrossRefGoogle Scholar
  24. Bennetzen JL, Swanson J, Taylor WC, Freeling M (1984) DNA insertion in the first intron of maize Adh1 affects message levels: cloning of progenitor and mutant Adh1 alleles. Proc Natl Acad Sci USA 81(13):4125–4128PubMedCrossRefGoogle Scholar
  25. Bennetzen JL, Coleman C, Liu R, Ma J, Ramakrishna W (2004) Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol 7(6):732–736PubMedCrossRefGoogle Scholar
  26. Bennetzen JL, Ma JX, Devos K (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95(1):127–132PubMedCrossRefGoogle Scholar
  27. Benovoy D, Drouin G (2006) Processed pseudogenes, processed genes, and spontaneous mutations in the Arabidopsis genome. J Mol Evol 62(5):511–522PubMedCrossRefGoogle Scholar
  28. Bergman CM, Quesneville H (2007) Discovering and detecting transposable elements in genome sequences. Brief Bioinform 8(6):382–392PubMedCrossRefGoogle Scholar
  29. Biemont C (2010) A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics 186(4):1085–1093PubMedCrossRefGoogle Scholar
  30. Blumenstiel JP (2010) Evolutionary dynamics of transposable elements in a small RNA world. Trends Genet 27(1):23–31PubMedCrossRefGoogle Scholar
  31. Bureau TE, Wessler SR (1992) Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 4(10):1283–1294PubMedCrossRefGoogle Scholar
  32. Bureau TE, Wessler SR (1994) Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6(6):907–916PubMedCrossRefGoogle Scholar
  33. C.elegans-Genome-Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282(5396):2012–2018CrossRefGoogle Scholar
  34. Callinan PA, Batzer MA (2006) Retrotransposable elements and human disease. Genome Dyn 1:104–115PubMedCrossRefGoogle Scholar
  35. Campagna D, Romualdi C, Vitulo N et al (2005) RAP: a new computer program for de novo identification of repeated sequences in whole genomes. Bioinformatics 21(5):582PubMedCrossRefGoogle Scholar
  36. Casacuberta E, Casacuberta JM, Puigdomenech P, Monfort A (1998) Presence of miniature inverted-repeat transposable elements (MITEs) in the genome of Arabidopsis thaliana: characterisation of the Emigrant family of elements. Plant J 16(1):79–85PubMedCrossRefGoogle Scholar
  37. Casola C, Hucks D, Feschotte C (2008) Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol Biol Evol 25(1):29–41PubMedCrossRefGoogle Scholar
  38. Cavalier-Smith T (1985) Selfish DNA and the origin of introns. Nature 315(6017):283–284PubMedCrossRefGoogle Scholar
  39. Chandler V, Rivin C, Walbot V (1986) Stable non-mutator stocks of maize have sequences homologous to the Mu1 transposable element. Genetics 114(3):1007–1021PubMedGoogle Scholar
  40. Charlesworth B, Charlesworth D (1983) The population-dynamics of transposable elements. Genet Res 42(1):1–27CrossRefGoogle Scholar
  41. Chen JM, Stenson PD, Cooper DN, Ferec C (2005) A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 117(5):411–427PubMedCrossRefGoogle Scholar
  42. Chen ZJ, Ha M, Soltis D (2007) Polyploidy: genome obesity and its consequences. New Phytol 174(4):717–720PubMedCrossRefGoogle Scholar
  43. Chen Y, Zhou F, Li G, Xu Y (2009) MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. Gene 436(1–2):1–7PubMedCrossRefGoogle Scholar
  44. Churakov G, Grundmann N, Kuritzin A, Brosius J, Makalowski W, Schmitz J (2010) A novel web-based TinT application and the chronology of the Primate Alu retroposon activity. BMC Evol Biol 10:376PubMedCrossRefGoogle Scholar
  45. Cohen CJ, Lock WM, Mager DL (2009) Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene 448(2):105–114PubMedCrossRefGoogle Scholar
  46. Crain WR, Davidson EH, Britten RJ (1976) Contrasting patterns of DNA sequence arrangement in Apis mellifera (honeybee) and Musca domestica (housefly). Chromosoma 59(1):1–12PubMedCrossRefGoogle Scholar
  47. Daniels GR, Fox GM, Loewensteiner D, Schmid CW, Deininger PL (1983) Species-specific homogeneity of the primate Alu family of repeated DNA sequences. Nucleic Acids Res 11(21):7579–7593PubMedCrossRefGoogle Scholar
  48. Daniels SB, Peterson KR, Strausbaugh LD, Kidwell MG, Chovnick A (1990) Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics 124(2):339–355PubMedGoogle Scholar
  49. Deceliere G, Charles S, Biemont C (2005) The dynamics of transposable elements in structured populations. Genetics 169(1):467–474PubMedCrossRefGoogle Scholar
  50. Deceliere G, Letrillard Y, Charles S, Biémont C (2006) TESD: a transposable element dynamics simulation environment. Bioinformatics 22(21):2702PubMedCrossRefGoogle Scholar
  51. Deininger PL, Jolly DJ, Rubin CM, Friedmann T, Schmid CW (1981) Base sequence studies of 300 nucleotide renatured repeated human DNA clones. J Mol Biol 151(1):17–33PubMedCrossRefGoogle Scholar
  52. Delcher AL, Phillippy A, Carlton J, Salzberg SL (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 30(11):2478–2483PubMedCrossRefGoogle Scholar
  53. Dewannieux M, Esnault C, Heidmann T (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35(1):41–48PubMedCrossRefGoogle Scholar
  54. Diao YP, Qi YM, Ma YJ et al (2011) Next-generation sequencing reveals recent horizontal transfer of a DNA transposon between divergent mosquitoes. PLoS One 6(2):e16743PubMedCrossRefGoogle Scholar
  55. Dolgin ES, Charlesworth B (2006) The fate of transposable elements in asexual populations. Genetics 174(2):817–827PubMedCrossRefGoogle Scholar
  56. Dolgin ES, Charlesworth B (2008) The effects of recombination rate on the distribution and abundance of transposable elements. Genetics 178(4):2169–2177PubMedCrossRefGoogle Scholar
  57. Doring HP, Starlinger P (1984) Barbara McClintock's controlling elements: now at the DNA level. Cell 39(2 Pt 1):253–259PubMedCrossRefGoogle Scholar
  58. Du C, Caronna J, He L, Dooner HK (2008) Computational prediction and molecular confirmation of Helitron transposons in the maize genome. BMC Genomics 9:51PubMedCrossRefGoogle Scholar
  59. Du C, Fefelova N, Caronna J, He L, Dooner HK (2009) The polychromatic Helitron landscape of the maize genome. Proc Natl Acad Sci USA 106(47):19916–19921PubMedGoogle Scholar
  60. Du J, Grant D, Tian Z et al (2010) SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics 11(1):113PubMedCrossRefGoogle Scholar
  61. Eckardt NA (2009) Pack-MULEs carry functionality. Plant Cell 21(1):15PubMedCrossRefGoogle Scholar
  62. Economou EP, Bergen AW, Warren AC, Antonarakis SE (1990) The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome. Proc Natl Acad Sci USA 87(8):2951–2954PubMedCrossRefGoogle Scholar
  63. Edgar RC, Myers EW (2005) PILER: identification and classification of genomic repeats. Bioinformatics 21:I152–I158PubMedCrossRefGoogle Scholar
  64. Eickbush TH, Furano AV (2002) Fruit flies and humans respond differently to retrotransposons. Curr Opin Genet Dev 12(6):669–674PubMedCrossRefGoogle Scholar
  65. Ellinghaus D, Kurtz S, Willhoeft U (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinforma 9(1):18CrossRefGoogle Scholar
  66. Evgen'ev MB, Zelentsova H, Poluectova H et al (2000) Mobile elements and chromosomal evolution in the virilis group of Drosophila. Proc Natl Acad Sci USA 97(21):11337–11342PubMedCrossRefGoogle Scholar
  67. Feng SH, Jacobsen SE, Reik W (2010) Epigenetic reprogramming in plant and animal development. Science 330(6004):622–627PubMedCrossRefGoogle Scholar
  68. Feschotte C (2004) Merlin, a new superfamily of DNA transposons identified in diverse animal genomes and related to bacterial IS1016 insertion sequences. Mol Biol Evol 21(9):1769–1780PubMedCrossRefGoogle Scholar
  69. Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9(5):397–405PubMedCrossRefGoogle Scholar
  70. Feschotte C, Mouches C (2000) Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. Mol Biol Evol 17(5):730–737PubMedGoogle Scholar
  71. Feschotte C, Pritham EJ (2005) Non-mammalian c-integrases are encoded by giant transposable elements. Trends Genet 21(10):551–552PubMedCrossRefGoogle Scholar
  72. Feschotte C, Wessler SR (2002) Mariner-like transposases are widespread and diverse in flowering plants. Proc Natl Acad Sci USA 99(1):280–285PubMedCrossRefGoogle Scholar
  73. Feschotte C, Keswani U, Ranganathan N, Guibotsy ML, Levine D (2009) Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes. Genome Biol Evol 1:205–220PubMedCrossRefGoogle Scholar
  74. Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5(4):103–107PubMedCrossRefGoogle Scholar
  75. Fischer MG, Suttle CA (2011) A virophage at the origin of large DNA transposons. Science. doi: 10.1126/science.1199412
  76. Fiston-Lavier AS, Anxolabehere D, Quesneville H (2007) A model of segmental duplication formation in Drosophila melanogaster. Genome Res 17(10):1458–1470PubMedCrossRefGoogle Scholar
  77. Fiston-Lavier AS, Carrigan M, Petrov DA, González J (2010) T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Nucleic Acids Res. doi: 10.1093/nar/gkq1291
  78. Flavell RB, Bennett MD, Smith JB, Smith DB (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12(4):257–269PubMedCrossRefGoogle Scholar
  79. Flutre T, Duprat E, Feuillet C, Quesneville H (2011) Considering transposable element diversification in de novo annotation approaches. PLoS One 6(1):e16526PubMedCrossRefGoogle Scholar
  80. Friz CT (1968) The biochemical composition of the free-living amoebae Chaos chaos, Amoeba dubia and Amoeba proteus. Comp Biochem Physiol 26(1):81–90PubMedCrossRefGoogle Scholar
  81. Fujino K, Hashida S, Ogawa T et al (2011) Temperature controls nuclear import of Tam3 transposase in Antirrhinum. Plant J 65(1):146–155PubMedCrossRefGoogle Scholar
  82. Gardner MJ, Hall N, Fung E et al (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419(6906):498–511PubMedCrossRefGoogle Scholar
  83. Germon S, Bouchet N, Casteret S et al (2009) Mariner Mos1 transposase optimization by rational mutagenesis. Genetica 137(3):265–276PubMedCrossRefGoogle Scholar
  84. Gilbert C, Schaack S, Pace JK 2nd, Brindley PJ, Feschotte C (2010) A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature 464(7293):1347–1350PubMedCrossRefGoogle Scholar
  85. Gilson PR, Su V, Slamovits CH, Reith ME, Keeling PJ, McFadden GI (2006) Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. Proc Natl Acad Sci USA 103(25):9566–9571PubMedCrossRefGoogle Scholar
  86. Giordano J, Ge Y, Gelfand Y, Abrusan G, Benson G, Warburton PE (2007) Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput Biol 3(7):e137PubMedCrossRefGoogle Scholar
  87. Girard L, Freeling M (1999) Regulatory changes as a consequence of transposon insertion. Dev Genet 25(4):291–296PubMedCrossRefGoogle Scholar
  88. Goff S, Ricke D, Lan T et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296(5565):92PubMedCrossRefGoogle Scholar
  89. Gogolevsky KP, Vassetzky NS, Kramerov DA (2008) Bov-B-mobilized SINEs in vertebrate genomes. Gene 407(1–2):75–85PubMedCrossRefGoogle Scholar
  90. Goodwin TJD, Butler MI, Poulter RTM (2003) Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi. Microbiology-Sgm 149:3099–3109CrossRefGoogle Scholar
  91. Gould SJ, Vrba ES (1982) Exaptation—a missing term in the science of form. Paleobiology 8(1):4–15Google Scholar
  92. Gregory TR (2001) The bigger the C-value, the larger the cell: genome size and red blood cell size in vertebrates. Blood Cells Mol Dis 27(5):830–843PubMedCrossRefGoogle Scholar
  93. Gregory TR, DeSalle R (2005) Comparative genomics in prokaryotes. In: Gregory TR (ed) The evolution of the genome. Elsevier, San Diego, pp 585–675Google Scholar
  94. Gregory TR, Nicol JA, Tamm H et al (2007) Eukaryotic genome size databases. Nucleic Acids Res 35(Database issue):D332–D338PubMedCrossRefGoogle Scholar
  95. Grover CE, Wendel JF (2010) Recent insights into mechanisms of genome size change in plants. J Botany 2010:382732. doi: 10.1155/2010/382732
  96. Grover CE, Hawkins JS, Wendel JF (2007) Tobacco genomes quickly go up in smoke. New Phytol 175(4):599–602PubMedCrossRefGoogle Scholar
  97. Gu W, Castoe T, Hedges D, Batzer M, Pollock D (2008) Identification of repeat structure in large genomes using repeat probability clouds. Anal Biochem 380(1):77–83PubMedCrossRefGoogle Scholar
  98. Han Y, Wessler SR (2010) MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res 38(22):e199PubMedCrossRefGoogle Scholar
  99. Hanada K, Vallejo V, Nobuta K et al (2009) The functional role of Pack-MULEs in rice inferred from purifying selection and expression profile. Plant Cell 21(1):25–38PubMedCrossRefGoogle Scholar
  100. Hancock CN, Zhang F, Wessler SR (2010) Transposition of the Tourist-MITE mPing in yeast: an assay that retains key features of catalysis by the class 2 PIF/Harbinger superfamily. Mob DNA 1(1):5PubMedCrossRefGoogle Scholar
  101. Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16(10):1252–1261PubMedCrossRefGoogle Scholar
  102. Haynes SR, Jelinek WR (1981) Low molecular weight RNAs transcribed in vitro by RNA polymerase III from Alu-type dispersed repeats in Chinese hamster DNA are also found in vivo. Proc Natl Acad Sci USA 78(10):6130–6134PubMedCrossRefGoogle Scholar
  103. Herron PR, Hughes G, Chandra G, Fielding S, Dyson PJ (2004) Transposon Express, a software application to report the identity of insertions obtained by comprehensive transposon mutagenesis of sequenced genomes: analysis of the preference for in vitro Tn5 transposition into GC-rich DNA. Nucleic Acids Res 32(14):e113PubMedCrossRefGoogle Scholar
  104. Hikosaka A, Kawahara A (2010) A systematic search and classification of T2 family miniature inverted-repeat transposable elements (MITEs) in Xenopus tropicalis suggests the existence of recently active MITE subfamilies. Mol Genet Genomics 283(1):49–62PubMedCrossRefGoogle Scholar
  105. Hill AS, Foot NJ, Chaplin TL, Young BD (2000) The most frequent constitutional translocation in humans, the t(11;22)(q23;q11) is due to a highly specific Alu-mediated recombination. Hum Mol Genet 9(10):1525–1532PubMedCrossRefGoogle Scholar
  106. Hoogland C, Biemont C (1997) DROSOPOSON: a knowledge base on chromosomal localization of transposable element insertions in Drosophila. Bioinformatics 13(1):61CrossRefGoogle Scholar
  107. Huda A, Jordan IK (2009) Epigenetic regulation of mammalian genomes by transposable elements. Ann N Y Acad Sci 1178:276–284PubMedCrossRefGoogle Scholar
  108. Izsvak Z, Ivics Z, Shimoda N, Mohn D, Okamoto H, Hackett PB (1999) Short inverted-repeat transposable elements in teleost fish and implications for a mechanism of their amplification. J Mol Evol 48(1):13–21PubMedCrossRefGoogle Scholar
  109. Jelinek WR, Schmid CW (1982) Repetitive sequences in eukaryotic DNA and their expression. Annu Rev Biochem 51:813–844PubMedCrossRefGoogle Scholar
  110. Jelinek WR, Toomey TP, Leinwand L et al (1980) Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc Natl Acad Sci USA 77(3):1398–1402PubMedCrossRefGoogle Scholar
  111. Jiang N, Bao Z, Zhang X et al (2003) An active DNA transposon family in rice. Nature 421(6919):163–167PubMedCrossRefGoogle Scholar
  112. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431(7008):569–573PubMedCrossRefGoogle Scholar
  113. Jurka J (1997) Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA 94(5):1872–1877PubMedCrossRefGoogle Scholar
  114. Jurka J, Kapitonov VV (2001) PiFs meet Tourists and Harbingers: a superfamily reunion. Proc Natl Acad Sci USA 98(22):12315–12316PubMedCrossRefGoogle Scholar
  115. Jurka J, Kapitonov V, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110(1–4):462–467PubMedCrossRefGoogle Scholar
  116. Kahn SD (2011) On the future of genomic data. Science 331(6018):728–729PubMedCrossRefGoogle Scholar
  117. Kajikawa M, Okada N (2002) LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111(3):433–444PubMedCrossRefGoogle Scholar
  118. Kalyanaraman A, Aluru S (2006) Efficient algorithms and software for detection of full-length LTR retrotransposons. J Bioinform Comput Biol 4(2):197–216PubMedCrossRefGoogle Scholar
  119. Kapitonov VV, Jurka J (2001) Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA 98(15):8714–8719PubMedCrossRefGoogle Scholar
  120. Kapitonov VV, Jurka J (2003) Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci USA 100(11):6569–6574PubMedCrossRefGoogle Scholar
  121. Kapitonov VV, Jurka J (2005) RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3(6):998–1011CrossRefGoogle Scholar
  122. Kapitonov VV, Jurka J (2007) Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 23(10):521–529PubMedCrossRefGoogle Scholar
  123. Kapitonov V, Jurka J (2008) A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 9(5):411–412PubMedCrossRefGoogle Scholar
  124. Kashkush K, Khasdan V (2007) Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 177(4):1975–1985PubMedCrossRefGoogle Scholar
  125. Khelifi A, Duret L, Mouchiroud D (2005) HOPPSIGEN: a database of human and mouse processed pseudogenes. Nucleic Acids Res 33(Database issue):D59–D66PubMedGoogle Scholar
  126. Khurana JS, Theurkauf W (2010) piRNAs, transposon silencing, and Drosophila germline development. J Cell Biol 191(5):905–913PubMedCrossRefGoogle Scholar
  127. Kidwell MG (2002) Transposable elements and the evolution of genome size in eukaryotes. Genetica 115(1):49–63PubMedCrossRefGoogle Scholar
  128. Kohany O, Gentles AJ, Hankus L, Jurka J (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinforma 7:474CrossRefGoogle Scholar
  129. Kojima KK, Fujiwara H (2005) Long-term inheritance of the 28S rDNA-specific retrotransposon R2. Mol Biol Evol 22(11):2157–2165PubMedCrossRefGoogle Scholar
  130. Kordis D, Gubensek F (1998) Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. Proc Natl Acad Sci USA 95(18):10704–10709PubMedCrossRefGoogle Scholar
  131. Koszul R, Caburet S, Dujon B, Fischer G (2004) Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J 23(1):234–243PubMedCrossRefGoogle Scholar
  132. Kramerov DA, Vassetzky NS (2005) Short retroposons in eukaryotic genomes. Int Rev Cytol 247:165–221PubMedCrossRefGoogle Scholar
  133. Kramerov DA, Grigoryan AA, Ryskov AP, Georgiev GP (1979) Long double-stranded sequences (dsRNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments. Nucleic Acids Res 6(2):697–713PubMedCrossRefGoogle Scholar
  134. Krayev AS, Kramerov DA, Skryabin KG, Ryskov AP, Bayev AA, Georgiev GP (1980) The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA. Nucleic Acids Res 8(6):1201–1215PubMedCrossRefGoogle Scholar
  135. Krayev AS, Markusheva TV, Kramerov DA et al (1982) Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing. Nucleic Acids Res 10(23):7461–7475PubMedCrossRefGoogle Scholar
  136. Kronmiller BA, Wise RP (2008) TEnest: automated chronological annotation and visualization of nested plant transposable elements. Plant Physiol 146(1):45–59PubMedCrossRefGoogle Scholar
  137. Kunarso G, Chia NY, Jeyakani J et al (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42(7):631-U111CrossRefGoogle Scholar
  138. Kurtz S, Choudhuri J, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29(22):4633PubMedCrossRefGoogle Scholar
  139. Kurtz S, Narechania A, Stein JC, Ware D (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9:517PubMedCrossRefGoogle Scholar
  140. Lai JS, Li YB, Messing J, Dooner HK (2005) Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci USA 102(25):9068–9073PubMedCrossRefGoogle Scholar
  141. Lal SK, Hannah LC (2005) Plant genomes—massive changes of the maize genome are caused by Helitrons. Heredity 95(6):421–422PubMedCrossRefGoogle Scholar
  142. Lander E, Linton L, Birren B et al (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921PubMedCrossRefGoogle Scholar
  143. Le Rouzic A, Capy P (2009) Theoretical approaches to the dynamics of transposable elements in genomes, populations, and species. In: Lankenau D-H, Volff J-N (eds) Transposons and the dynamic genome. Springer, Berlin, pp 1–19Google Scholar
  144. Le Rouzic A, Deceliere G (2005) Models of the population genetics of transposable elements. Genet Res 85(3):171–181PubMedCrossRefGoogle Scholar
  145. Le Rouzic A, Boutin TS, Capy P (2007) Long-term evolution of transposable elements. Proc Natl Acad Sci USA 104(49):19375–19380PubMedCrossRefGoogle Scholar
  146. Lefebvre A, Lecroq T, Dauchel H, Alexandre J (2003) FORRepeats: detects repeats on entire chromosomes and between genomes. Bioinformatics 19(3):319–326PubMedCrossRefGoogle Scholar
  147. Lerat E (2009) Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity 104(6):520–533PubMedCrossRefGoogle Scholar
  148. Levy A, Sela N, Ast G (2008) TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res 36(Database issue):D47PubMedGoogle Scholar
  149. Li M, Ma B, Kisman D, Tromp J (2004) Patternhunter II: highly sensitive and fast homology search. J Bioinform Comput Biol 2(3):417–439PubMedCrossRefGoogle Scholar
  150. Li R, Ye J, Li S et al (2005) ReAS: recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1(4):E43PubMedCrossRefGoogle Scholar
  151. Li X, Kahveci T, Settles A (2008) A novel genome-scale repeat finder geared towards transposons. Bioinformatics 24(4):468PubMedCrossRefGoogle Scholar
  152. Lin RC, Ding L, Casola C, Ripoll DR, Feschotte C, Wang HY (2007) Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318(5854):1302–1305PubMedCrossRefGoogle Scholar
  153. Lisch D (2009) Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60:43–66PubMedCrossRefGoogle Scholar
  154. Llorens C, Futami R, Covelli L et al (2010) The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res 39(Database issue):D70–D74PubMedGoogle Scholar
  155. Lorenzi H, Thiagarajan M, Haas B, Wortman J, Hall N, Caler E (2008) Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species. BMC Genomics 9(1):595PubMedCrossRefGoogle Scholar
  156. Loreto EL, Carareto CM, Capy P (2008) Revisiting horizontal transfer of transposable elements in Drosophila. Heredity 100(6):545–554PubMedCrossRefGoogle Scholar
  157. Lozovskaya ER, Hartl DL, Petrov DA (1995) Genomic regulation of transposable elements in Drosophila. Curr Opin Genet Dev 5(6):768–773PubMedCrossRefGoogle Scholar
  158. Lu J, Clark AG (2009) Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. Genome Res 20(2):212–227PubMedCrossRefGoogle Scholar
  159. Lucier JF, Perreault J, Noel JF, Boire G, Perreault JP (2007) RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures. Nucleic Acids Res 35(Web Server issue):W269–W274PubMedCrossRefGoogle Scholar
  160. Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14(5):860–869PubMedCrossRefGoogle Scholar
  161. Maksakova IA, Romanish MT, Gagnier L, Dunn CA, de Lagemaat LNV, Mager DL (2006) Retroviral elements and their hosts: Insertional mutagenesis in the mouse germ line. PLoS Genet 2(1):1–10CrossRefGoogle Scholar
  162. Malik HS, Burke WD, Eickbush TH (1999) The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol 16(6):793–805PubMedGoogle Scholar
  163. Marques AC, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H (2005) Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 3(11):1970–1979CrossRefGoogle Scholar
  164. Maruyama K, Hartl DL (1991) Evidence for interspecific transfer of the transposable element mariner between Drosophila and Zaprionus. J Mol Evol 33(6):514–524PubMedCrossRefGoogle Scholar
  165. McCarthy EM, McDonald JF (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19(3):362–367PubMedCrossRefGoogle Scholar
  166. McClintock B (1948) Mutable loci in maize. Carnegie Institute of Washington Year Book 47:155–169Google Scholar
  167. McClintock B (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA 36(6):344–355PubMedCrossRefGoogle Scholar
  168. McPherson JD, Marra M, Hillier L et al (2001) A physical map of the human genome. Nature 409(6822):934–941PubMedCrossRefGoogle Scholar
  169. Medstrand P, van de Lagemaat LN, Dunn CA, Landry JR, Svenback D, Mager DL (2005) Impact of transposable elements on the evolution of mammalian gene regulation. Cytogenet Genome Res 110(1–4):342–352PubMedCrossRefGoogle Scholar
  170. Miskey C, Izsvak Z, Plasterk RH, Ivics Z (2003) The Frog Prince: a reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells. Nucleic Acids Res 31(23):6873–6881PubMedCrossRefGoogle Scholar
  171. Miskey C, Papp B, Mates L et al (2007) The ancient mariner sails again: Transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. Mol Cell Biol 27(12):4589–4600PubMedCrossRefGoogle Scholar
  172. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37(9):997–1002PubMedCrossRefGoogle Scholar
  173. Naik PK, Mittal VK, Gupta S (2008) RetroPred: a tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs & SINEs) from the genome by integrating PALS, PILER, MEME and ANN. Bioinformation 2(6):263PubMedGoogle Scholar
  174. Naito K, Zhang F, Tsukiyama T et al (2009) Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Genes Genet Syst 84(6):439Google Scholar
  175. Neumann P, Koblizkova A, Navratilova A, Macas J (2006) Significant expansion of Vicia pannonica genome size mediated by amplification of a single type of giant retroelement. Genetics 173(2):1047–1056PubMedCrossRefGoogle Scholar
  176. Nicolas J, Durand P, Ranchy G, Tempel S, Valin A (2005) Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes. Bioinformatics 21(24):4408PubMedCrossRefGoogle Scholar
  177. Novak P, Neumann P, Macas J (2010) Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinforma 11(1):378CrossRefGoogle Scholar
  178. Okada N, Hamada M, Ogiwara I, Ohshima K (1997) SINEs and LINEs share common 3′ sequences: a review. Gene 205(1–2):229–243PubMedCrossRefGoogle Scholar
  179. Oliver KR, Greene WK (2009) Transposable elements: powerful facilitators of evolution. Bioessays 31(7):703–714PubMedCrossRefGoogle Scholar
  180. Otto TD, Gomes LHF, Alves-Ferreira M, De Miranda AB, Degrave WM (2008) ReRep: computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinforma 9(1):366CrossRefGoogle Scholar
  181. Paces J, Pavlícek A, Paces V (2002) HERVd: database of human endogenous retroviruses. Nucleic Acids Res 30(1):205PubMedCrossRefGoogle Scholar
  182. Parisod C, Alix K, Just J et al (2009) Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol 186(1):37–45PubMedCrossRefGoogle Scholar
  183. Pellicer J, Fay MF, Leitch IJ (2010) The largest eukaryotic genome of them all? Bot J Linn Soc 164(1):10–15CrossRefGoogle Scholar
  184. Pennisi E (2011) Human genome 10th anniversary. will computers crash genomics? Science 331(6018):666–668PubMedCrossRefGoogle Scholar
  185. Pereira V (2004) Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol 5(10):R79PubMedCrossRefGoogle Scholar
  186. Pereira V (2008) Automated paleontology of repetitive DNA with REANNOTATE. BMC Genomics 9(1):614PubMedCrossRefGoogle Scholar
  187. Perez-Iratxeta C, Palidwor G, Andrade-Navarro MA (2007) Towards completion of the Earth's proteome. EMBO Rep 8(12):1135–1141PubMedCrossRefGoogle Scholar
  188. Peterson-Burch BD, Nettleton D, Voytas DF (2004) Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae. Genome Biol 5(10):R78PubMedCrossRefGoogle Scholar
  189. Pevzner PA, Tang HX, Tesler G (2004) De novo repeat classification and fragment assembly. Genome Res 14(9):1786–1796PubMedCrossRefGoogle Scholar
  190. Piegu B, Guyot R, Picault N et al (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16(10):1262–1269PubMedCrossRefGoogle Scholar
  191. Piriyapongsa J, Jordan IK (2007) A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS One 2(2):e203PubMedCrossRefGoogle Scholar
  192. Piriyapongsa J, Jordan IK (2008) Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14(5):814–821PubMedCrossRefGoogle Scholar
  193. Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21:I351–I358PubMedCrossRefGoogle Scholar
  194. Pritham EJ, Feschotte C (2007) Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci USA 104(6):1895–1900PubMedCrossRefGoogle Scholar
  195. Pritham EJ, Putliwala T, Feschotte C (2007) Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 390(1–2):3–17PubMedCrossRefGoogle Scholar
  196. Quesneville H, Bergman CM, Andrieu O et al (2005a) Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol 1(2):166–175PubMedCrossRefGoogle Scholar
  197. Quesneville H, Nouaud D, Anxolabehere D (2005b) Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-transposable element. Mol Biol Evol 22(3):741–746PubMedCrossRefGoogle Scholar
  198. Rangwala SH, Kazazian HH (2009) The L1 retrotransposition assay: a retrospective and toolkit. Methods 49(3):219–226PubMedCrossRefGoogle Scholar
  199. Ray DA, Feschotte C, Pagan HJT et al (2008) Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Res 18(5):717–728PubMedCrossRefGoogle Scholar
  200. Reiss D, Zhang Y, Rouhi A, Reuter M, Mager DL (2010) Variable DNA methylation of transposable elements: the case study of mouse early transposons. Epigenetics 5(1):68–79PubMedCrossRefGoogle Scholar
  201. Rho M, Tang H (2009) MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes. Nucleic Acids Res 37(21):e143PubMedCrossRefGoogle Scholar
  202. Rho M, Choi JH, Kim S, Lynch M, Tang H (2007) De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics 8:90PubMedCrossRefGoogle Scholar
  203. Romanish MT, Lock WM, van de Lagemaat LN, Dunn CA, Mager DL (2007) Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. Plos Genet 3(1):e10Google Scholar
  204. Rooke R, Yang G (2011) TE Displayer for post-genomic analysis of transposable elements. Bioinformatics 27(2):286–287PubMedCrossRefGoogle Scholar
  205. Rowold DJ, Herrera RJ (2000) Alu elements and the human genome. Genetica 108(1):57–72PubMedCrossRefGoogle Scholar
  206. Saha S, Bridges S, Magbanua Z, Peterson D (2008a) Computational approaches and tools used in identification of dispersed repetitive DNA sequences. Tropical Plant Biology 1(1):85–96CrossRefGoogle Scholar
  207. Saha S, Bridges S, Magbanua ZV, Peterson DG (2008b) Empirical comparison of ab initio repeat finding programs. Nucleic Acids Res 36(7):2284–2294PubMedCrossRefGoogle Scholar
  208. Saito K, Siomi MC (2010) Small RNA-mediated quiescence of transposable elements in animals. Dev Cell 19(5):687–697PubMedCrossRefGoogle Scholar
  209. Sanchez-Gracia A, Maside X, Charlesworth B (2005) High rate of horizontal transfer of transposable elements in Drosophila. Trends Genet 21(4):200–203PubMedCrossRefGoogle Scholar
  210. Schaack S, Gilbert C, Feschotte C (2010) Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol 25(9):537–546PubMedCrossRefGoogle Scholar
  211. Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115PubMedCrossRefGoogle Scholar
  212. Shapiro JA (1969) Mutations caused by insertion of genetic material into galactose operon of Escherichia coli. J Mol Biol 40(1):93PubMedCrossRefGoogle Scholar
  213. Shedlock AM, Okada N (2000) SINE insertions: powerful tools for molecular systematics. Bioessays 22(2):148–160PubMedCrossRefGoogle Scholar
  214. Silva JC, Loreto EL, Clark JB (2004) Factors that affect the horizontal transfer of transposable elements. Curr Issues Mol Biol 6(1):57–71PubMedGoogle Scholar
  215. Simmons GM (1992) Horizontal transfer of hobo transposable elements within the Drosophila melanogaster species complex: evidence from DNA sequencing. Mol Biol Evol 9(6):1050–1060PubMedGoogle Scholar
  216. Singh V, Mishra RK (2010) RISCI—repeat induced sequence changes identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes. BMC Bioinforma 11(1):609CrossRefGoogle Scholar
  217. Slotkin R, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8(4):272–285PubMedCrossRefGoogle Scholar
  218. Smit A, Hubley R (2010) 2008–2010. RepeatModeler Open-1.0.
  219. Smit A, Hubley R, Green P (2006) 1996–2004. RepeatMasker Open-3.0.
  220. Spannagl M, Haberer G, Ernst R, Schoof H, Mayer KF (2007) MIPS plant genome information resources. Methods Mol Biol 406:137–159PubMedCrossRefGoogle Scholar
  221. Sperber G, Airola T, Jern P, Blomberg J (2007) Automated recognition of retroviral sequences in genomic data RetroTector (C). Nucleic Acids Res 35:4964–4976Google Scholar
  222. Sperber G, Lovgren A, Eriksson NE, Benachenhou F, Blomberg J (2009) RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences. BMC Bioinforma 10(Suppl 6):S4CrossRefGoogle Scholar
  223. Stein LD (2010) The case for cloud computing in genome informatics. Genome Biol 11(5):207PubMedCrossRefGoogle Scholar
  224. Sulston J, Du Z, Thomas K et al (1992) The C. elegans genome sequencing project: a beginning. Nature 356(6364):37–41PubMedCrossRefGoogle Scholar
  225. Surzycki SA, Belknap WR (2000) Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes. Proc Natl Acad Sci USA 97(1):245–249PubMedCrossRefGoogle Scholar
  226. Szak ST, Pickeral OK, Makalowski W, Boguski MS, Landsman D, Boeke JD (2002) Molecular archeology of L1 insertions in the human genome. Genome Biol 3(10):research0052Google Scholar
  227. Takagi K, Ishikawa N, Maekawa M, Tsugane K, Iida S (2007) Transposon display for active DNA transposons in rice. Genes Genet Syst 82(2):109–122PubMedCrossRefGoogle Scholar
  228. Talbert LE, Chandler VL (1988) Characterization of a highly conserved sequence related to mutator transposable elements in maize. Mol Biol Evol 5(5):519–529PubMedGoogle Scholar
  229. Taylor LP, Walbot V (1987) Isolation and characterization of a 1.7-kb transposable element from a mutator line of maize. Genetics 117(2):297–307PubMedGoogle Scholar
  230. Tempel S, Jurka M, Jurka J (2008) VisualRepbase: an interface for the study of occurrences of transposable element families. BMC Bioinforma 9(1):345CrossRefGoogle Scholar
  231. Tempel S, Rousseau C, Tahi F, Nicolas J (2010) ModuleOrganizer: detecting modules in families of transposable elements. BMC Bioinforma 11(1):474CrossRefGoogle Scholar
  232. Tenaillon MI, Hollister JD, Gaut BS (2010) A triptych of the evolution of plant transposable elements. Trends Plant Sci 15(8):471–478PubMedCrossRefGoogle Scholar
  233. Thibaud-Nissen F, Shu OY, Buell R (2009) Identification and characterization of pseudogenes in the rice gene complement. BMC Genom 10:317Google Scholar
  234. Tóth G, Deák G, Barta E, Kiss G (2006) PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats. Nucleic Acids Res 34(Web Server issue):W708PubMedCrossRefGoogle Scholar
  235. Tu Z (2000) Molecular and evolutionary analysis of two divergent subfamilies of a novel miniature inverted repeat transposable element in the yellow fever mosquito, Aedes aegypti. Mol Biol Evol 17(9):1313–1325PubMedGoogle Scholar
  236. Tu Z (2001) Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. Proc Natl Acad Sci USA 98(4):1699PubMedCrossRefGoogle Scholar
  237. Tu Z, Coates C (2004) Mosquito transposable elements. Insect Biochem Mol Biol 34(7):631–644PubMedCrossRefGoogle Scholar
  238. Tu Z, Li S, Mao C (2004) The changing tails of a novel short interspersed element in Aedes aegypti: genomic evidence for slippage retrotransposition and the relationship between 3′ tandem repeats and the poly(dA) tail. Genetics 168(4):2037–2047PubMedCrossRefGoogle Scholar
  239. Van den Broeck D, Maes T, Sauer M et al (1998) Transposon display identifies individual transposable elements in high copy number lines. Plant J 13(1):121–129PubMedGoogle Scholar
  240. Venturini G, Capanna E, Fontana B (1987) Size and structure of the bird genome. II. Repetitive DNA and sequence organization. Comp Biochem Physiol B 87(4):975–979PubMedCrossRefGoogle Scholar
  241. Vitte C, Panaud O (2005) LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 110(1–4):91–107PubMedCrossRefGoogle Scholar
  242. Vitte C, Panaud O, Quesneville H (2007) LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics 8:218PubMedCrossRefGoogle Scholar
  243. Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P (2006) dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat 27(4):323–329PubMedCrossRefGoogle Scholar
  244. Weiner AM, Deininger PL, Efstratiadis A (1986) Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem 55:631–661PubMedCrossRefGoogle Scholar
  245. Wicker T, Matthews DE, Keller B (2002) TREP: a database for Triticeae repetitive elements. Trends Plant Sci 7(12):561–562CrossRefGoogle Scholar
  246. Wicker T, Sabot F, Hua-Van A et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8(12):973–982PubMedCrossRefGoogle Scholar
  247. Xu Z, Wang H (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35(Web Server issue):W265–W268PubMedCrossRefGoogle Scholar
  248. Yang L, Bennetzen JL (2009a) Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci 106(47):19922PubMedGoogle Scholar
  249. Yang L, Bennetzen JL (2009b) Structure-based discovery and description of plant and animal Helitrons. Proc Natl Acad Sci USA 106(31):12832–12837PubMedCrossRefGoogle Scholar
  250. Yang G, Hall T (2003a) MAK, a computational tool kit for automated MITE analysis. Nucleic Acids Res 31(13):3659PubMedCrossRefGoogle Scholar
  251. Yang G, Hall TC (2003b) MDM-1 and MDM-2: two mutator-derived MITE families in rice. J Mol Evol 56(3):255–264PubMedCrossRefGoogle Scholar
  252. Yang G, Dong J, Chandrasekharan MB, Hall TC (2001) Kiddo, a new transposable element family closely associated with rice genes. Mol Genet Genomics 266(3):417–424PubMedCrossRefGoogle Scholar
  253. Yang GJ, Weil CF, Wessler SR (2006) A rice TC1/mariner-like element transposes in yeast. Plant Cell 18(10):2469–2478PubMedCrossRefGoogle Scholar
  254. Yang G, Zhang F, Hancock CN, Wessler SR (2007) Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc Natl Acad Sci USA 104(26):10962–10967PubMedCrossRefGoogle Scholar
  255. Yang G, Nagel D, Feschotte C, Hancock C, Wessler S (2009) Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE. Science 325(5946):1391PubMedCrossRefGoogle Scholar
  256. Yant SR, Huang Y, Akache B, Kay MA (2007) Site-directed transposon integration in human cells. Nucleic Acids Res 35(7):e50PubMedCrossRefGoogle Scholar
  257. Yu Z, Wright SI, Bureau TE (2000) Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution. Genetics 156(4):2019–2031PubMedGoogle Scholar
  258. Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296(5565):5579CrossRefGoogle Scholar
  259. Zhang Y, Zaki MJ (2006) SMOTIF: efficient structured pattern and profile motif search. Algorithms Mol Biol 1(1):22PubMedCrossRefGoogle Scholar
  260. Zhang XY, Feschotte C, Zhang Q, Jiang N, Eggleston WB, Wessler SR (2001) P instability factor: an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc Natl Acad Sci USA 98(22):12572–12577PubMedCrossRefGoogle Scholar
  261. Zhang ZL, Harrison PM, Liu Y, Gerstein M (2003) Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 13(12):2541–2558PubMedCrossRefGoogle Scholar
  262. Zhang ZL, Carriero N, Gerstein M (2004) Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet 20(2):62–67PubMedCrossRefGoogle Scholar
  263. Zhou F, Xu Y (2009) RepPop: a database for repetitive elements in Populus trichocarpa. BMC Genomics 10(1):14PubMedCrossRefGoogle Scholar
  264. Zupunski V, Gubensek F, Kordis D (2001) Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons. Mol Biol Evol 18(10):1849–1863PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Mateusz Janicki
    • 1
    • 2
  • Rebecca Rooke
    • 1
    • 2
  • Guojun Yang
    • 1
    • 2
  1. 1.Department of BiologyUniversity of Toronto at MississaugaMississaugaCanada
  2. 2.Cell and Systems BiologyUniversity of TorontoTorontoCanada

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