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Helitron Proliferation and Gene-Fragment Capture

  • Yubin Li
  • Hugo K. Dooner
Chapter
Part of the Topics in Current Genetics book series (TCG, volume 24)

Abstract

Helitrons stand out as rare transposons discovered by bioinformatic, rather than genetic, studies. Although they comprise an ancient superfamily of transposons found in plants, animals, and fungi, it is in plants where they have been studied most extensively. Well-annotated plant genomes contain increasingly higher numbers of identified Helitrons, including putative autonomous elements and nonautonomous elements with and without gene fragments. The molecular structure of the autonomous Helitron and the postulated rolling circle mode of transposition remain hypothetical, and recent evidence suggests that Helitrons may transpose by both copy-and-paste and cut-and-paste mechanisms. Two Helitron properties, in particular, have caught the imagination of biologists: their ability to undergo sudden bursts of transposition and their ability to capture fragments from different genes to make chimeric transcripts. In this chapter, we provide an overview of what we have learned in the past decade about the biology of these intriguing, newly discovered plant genome residents.

Keywords

Helitrons Transposons Plants 

References

  1. Ahmed I, Sarazin A, Bowler C, Colot V, Quesneville H (2011) Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res 39:6919–6931PubMedCrossRefGoogle Scholar
  2. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  3. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M et al (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332:960–963PubMedCrossRefGoogle Scholar
  4. Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15:621–627PubMedCrossRefGoogle Scholar
  5. Berger N, Dubreucq B, Roudier F, Dubos C, Lepiniec L (2011) Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of Histone H3 at Lysine-27. Plant Cell 23:4065–4078PubMedCrossRefGoogle Scholar
  6. Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A (2005a) Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17:343–360PubMedCrossRefGoogle Scholar
  7. Brunner S, Pea G, Rafalski A (2005b) Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize. Plant J 43:799–810PubMedCrossRefGoogle Scholar
  8. Buti M, Giordani T, Cattonaro F, Cossu RM, Pistelli L et al (2011) Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions. Theor Appl Genet 123:779–791PubMedCrossRefGoogle Scholar
  9. Cho SH, Addo-Quaye C, Coruh C, Arif MA, Ma Z et al (2008) Physcomitrella patens DCL3 is required for 22–24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development. PLoS Genet 4:e1000314PubMedCrossRefGoogle Scholar
  10. Choi JD, Hoshino A, Park KI, Park IS, Iida S (2007) Spontaneous mutations caused by a Helitron transposon, Hel-It1, in morning glory, Ipomoea tricolor. Plant J 49:924–934PubMedCrossRefGoogle Scholar
  11. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J et al (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22:1686–1701PubMedCrossRefGoogle Scholar
  12. Chuck G, Meeley R, Irish E, Sakai H, Hake S (2007) The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nat Genet 39:1517–1521PubMedCrossRefGoogle Scholar
  13. Cocca E, De Iorio S, Capriglione T (2011) Identification of a novel helitron transposon in the genome of Antarctic fish. Mol Phylogenet Evol 58:439–446PubMedCrossRefGoogle Scholar
  14. Craig NL (2002) Tn7. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM Press, Washington, D.C., pp 422–456Google Scholar
  15. Craig NL, Craigie R, Gellert M, Lambowitz AM (2002) Mobile DNA II. ASM Press, Washington, D.CGoogle Scholar
  16. Dooner HK, Weil CF (2007) Give-and-take: interactions between DNA transposons and their host plant genomes. Curr Opin Genet Dev 17:486–492PubMedCrossRefGoogle Scholar
  17. Dooner HK, Weil CF (2012) Transposons and gene creation. In: Fedoroff N (ed) Molecular genetics and epigenetics of plant transposons: sculpting genes and genomes. Wiley, Hoboken, NJGoogle Scholar
  18. Doutriaux MP, Couteau F, Bergounioux C, White C (1998) Isolation and characterisation of the RAD51 and DMC1 homologs from Arabidopsis thaliana. Mol Gen Genet 257:283–291PubMedCrossRefGoogle Scholar
  19. 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
  20. Du C, Fefelova N, Caronna J, He L, Dooner HK (2009) The polychromatic Helitron landscape of the maize genome. Proc Natl Acad Sci USA 106:19916–19920PubMedGoogle Scholar
  21. Du J, Grant D, Tian Z, Nelson RT, Zhu L et al (2010) SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics 11:113PubMedCrossRefGoogle Scholar
  22. Fan C, Zhang Y, Yu Y, Rounsley S, Long M et al (2008) The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice. Mol Plant 1:839–850PubMedCrossRefGoogle Scholar
  23. Feschotte C, Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331–368PubMedCrossRefGoogle Scholar
  24. Feschotte C, Pritham EJ (2009) A cornucopia of Helitrons shapes the maize genome. Proc Natl Acad Sci USA 106:19747–19748PubMedGoogle Scholar
  25. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341PubMedCrossRefGoogle Scholar
  26. 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
  27. Fu H, Dooner HK (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci USA 99:9573–9578PubMedGoogle Scholar
  28. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D’Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438:1105–1115PubMedCrossRefGoogle Scholar
  29. Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, Goldberg RB, Fischer RL (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124:495–506PubMedCrossRefGoogle Scholar
  30. Gehring M, Bubb KL, Henikoff S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324:1447–1451PubMedCrossRefGoogle Scholar
  31. Gill N, SanMiguel P, Dhillon BDS, Abernathy B, Kim H et al (2010) Dynamic Oryza genomes: repetitive DNA sequences as genome modeling agents. Rice 3:251–269CrossRefGoogle Scholar
  32. Greco R, Ouwerkerk PB, Pereira A (2005) Suppression of an atypically spliced rice CACTA transposon transcript in transgenic plants. Genetics 169:2383–2387PubMedCrossRefGoogle Scholar
  33. Gui YJ, Zhou Y, Wang Y, Wang S, Wang SY, Hu Y, Bo SP, Chen H, Zhou CP, Ma NX, Zhang TZ, Fan LJ (2010) Insights into the bamboo genome: syntenic relationships to rice and sorghum. J Integr Plant Biol 52:1008–1015PubMedCrossRefGoogle Scholar
  34. Gupta S, Gallavotti A, Stryker GA, Schmidt RJ, Lal SK (2005) A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes. Plant Mol Biol 57:115–127PubMedCrossRefGoogle Scholar
  35. He L, Dooner HK (2009) Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions. Proc Natl Acad Sci USA 106:8410–8416PubMedCrossRefGoogle Scholar
  36. Holligan D, Zhang X, Jiang N, Pritham EJ, Wessler SR (2006) The transposable element landscape of the model legume Lotus japonicus. Genetics 174:2215–2228PubMedCrossRefGoogle Scholar
  37. Hollister JD, Gaut BS (2007) Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana. Mol Biol Evol 24:2515–2524PubMedCrossRefGoogle Scholar
  38. Hollister JD, Gaut BS (2009) Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res 19:1419–1428PubMedCrossRefGoogle Scholar
  39. Hollister JD, Smith LM, Guo YL, Ott F, Weigel D, Gaut BS (2011) Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci USA 108:2322–2327PubMedCrossRefGoogle Scholar
  40. Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 43:476–481PubMedCrossRefGoogle Scholar
  41. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EA, Wu Y, Guo J, He J, Jia Z, Ren Y, Tian G, Lu Y, Ruan J, Qian W, Wang M, Huang Q, Li B, Xuan Z, Cao J, Asan WZ, Zhang J, Cai Q, Bai Y, Zhao B, Han Y, Li Y, Li X, Wang S, Shi Q, Liu S, Cho WK, Kim JY, Xu Y, Heller-Uszynska K, Miao H, Cheng Z, Zhang S, Wu J, Yang Y, Kang H, Li M, Liang H, Ren X, Shi Z, Wen M, Jian M, Yang H, Zhang G, Yang Z, Chen R, Liu S, Li J, Ma L, Liu H, Zhou Y, Zhao J, Fang X, Li G, Fang L, Li Y, Liu D, Zheng H, Zhang Y, Qin N, Li Z, Yang G, Yang S, Bolund L, Kristiansen K, Zheng H, Li S, Zhang X, Yang H, Wang J, Sun R, Zhang B, Jiang S, Wang J, Du Y, Li S (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281PubMedCrossRefGoogle Scholar
  42. International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768CrossRefGoogle Scholar
  43. Ivics Z, Hackett PB, Plasterk RH, Izsvak Z (1997) Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91:501–510PubMedCrossRefGoogle Scholar
  44. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quétier F, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467PubMedCrossRefGoogle Scholar
  45. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569–573PubMedCrossRefGoogle Scholar
  46. Kapitonov VV, Jurka J (1999) Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica 107:27–37PubMedCrossRefGoogle Scholar
  47. Kapitonov VV, Jurka J (2001) Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA 98:8714–8719PubMedCrossRefGoogle Scholar
  48. Kapitonov VV, Jurka J (2007) Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 23:521–529PubMedCrossRefGoogle Scholar
  49. Kapitonov VV, Jurka J (2008) A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 9:411–412, author reply 414PubMedCrossRefGoogle Scholar
  50. Kermicle JL (1970) Dependence of the R-mottled aleurone phenotype in maize on mode of sexual transmission. Genetics 66:69–85PubMedGoogle Scholar
  51. Lai J, Li Y, Messing J, Dooner HK (2005) Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci USA 102:9068–9073PubMedCrossRefGoogle Scholar
  52. Lal SK, Giroux MJ, Brendel V, Vallejos CE, Hannah LC (2003) The maize genome contains a Helitron insertion. Plant Cell 15:381–391PubMedCrossRefGoogle Scholar
  53. Lal SK, Georgelis N, Hannah LC (2009a) Helitrons: their impact on maize genome evolution and diversity. In: Bennetzen JL, Hake SC (eds) Handbook of maize: genetics and genome, vol 2. Springer, New York, pp 329–339Google Scholar
  54. Lal SK, Oetjens M, Hannah LC (2009b) Helitrons: enigmatic abductors and mobilizers of host genome sequences. Plant Sci 176:181–186CrossRefGoogle Scholar
  55. Langdon T, Thomas A, Huang L, Farrar K, King J, Armstead I (2009) Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne. BMC Plant Biol 9:70PubMedCrossRefGoogle Scholar
  56. Le QH, Wright S, Yu Z, Bureau T (2000) Transposon diversity in Arabidopsis thaliana. Proc Natl Acad Sci USA 97:7376–7381PubMedCrossRefGoogle Scholar
  57. Levin HL, Moran JV (2011) Dynamic interactions between transposable elements and their hosts. Nat Rev Genet 12:615–627PubMedCrossRefGoogle Scholar
  58. Li Y, Dooner HK (2009) Excision of Helitron transposons in maize. Genetics 182:399–402PubMedCrossRefGoogle Scholar
  59. Lisch D (2009) Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60:43–66PubMedCrossRefGoogle Scholar
  60. Liu P, Sherman-Broyles S, Nasrallah ME, Nasrallah JB (2007) A cryptic modifier causing transient self-incompatibility in Arabidopsis thaliana. Curr Biol 17:734–740PubMedCrossRefGoogle Scholar
  61. Lockton S, Gaut BS (2009) The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana. J Mol Evol 68:80–89PubMedCrossRefGoogle Scholar
  62. Lockton S, Gaut BS (2010) The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata. BMC Evol Biol 10:10PubMedCrossRefGoogle Scholar
  63. McClintock B (1947) Cytogenetic studies of maize and Neurospora. Carnegie Inst Wash Yearbook 46:146–152Google Scholar
  64. McClintock B (1952) Chromosome organization and gene expression. Cold Spring Harb Symp Quant Biol 16:13–47CrossRefGoogle Scholar
  65. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–996PubMedCrossRefGoogle Scholar
  66. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A et al (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37:997–1002PubMedCrossRefGoogle Scholar
  67. Naito K, Cho E, Yang G, Campbell MA, Yano K, Okumoto Y, Tanisaka T, Wessler SR (2006) Dramatic amplification of a rice transposable element during recent domestication. Proc Natl Acad Sci USA 103:17620–17625PubMedCrossRefGoogle Scholar
  68. Numa H, Kim JM, Matsui A, Kurihara Y, Morosawa T, Ishida J, Mochizuki Y, Kimura H, Shinozaki K, Toyoda T, Seki M, Yoshikawa M, Habu Y (2010) Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana. EMBO J 29:352–362PubMedCrossRefGoogle Scholar
  69. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman WD, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556PubMedCrossRefGoogle Scholar
  70. Pritham EJ, Feschotte C (2007) Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci USA 104:1895–1900PubMedCrossRefGoogle Scholar
  71. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319:64–69PubMedCrossRefGoogle Scholar
  72. Scherrer B, Isidore E, Klein P, Kim JS, Bellec A, Chalhoub B, Keller B, Feuillet C (2005) Large intraspecific haplotype variability at the Rph7 locus results from rapid and recent divergence in the barley genome. Plant Cell 17:361–374PubMedCrossRefGoogle Scholar
  73. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183PubMedCrossRefGoogle Scholar
  74. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115PubMedCrossRefGoogle Scholar
  75. Sherman-Broyles S, Boggs N, Farkas A, Liu P, Vrebalov J, Nasrallah ME, Nasrallah JB (2007) S locus genes and the evolution of self-fertility in Arabidopsis thaliana. Plant Cell 19:94–106PubMedCrossRefGoogle Scholar
  76. Shirzadi R, Andersen ED, Bjerkan KN, Gloeckle BM, Heese M, Ungru A, Winge P, Koncz C, Aalen RB, Schnittger A, Grini PE (2011) Genome-wide transcript profiling of endosperm without paternal contribution identifies parent-of-origin-dependent regulation of AGAMOUS-LIKE36. PLoS Genet 7:e1001303PubMedCrossRefGoogle Scholar
  77. Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, Feijó JA, Martienssen RA (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136:461–472PubMedCrossRefGoogle Scholar
  78. Song R, Messing J (2003) Gene expression of a gene family in maize based on noncollinear haplotypes. Proc Natl Acad Sci USA 100:9055–9060PubMedCrossRefGoogle Scholar
  79. Spillane C, Baroux C, Escobar-Restrepo JM, Page DR, Laoueille S, Grossniklaus U (2004) Transposons and tandem repeats are not involved in the control of genomic imprinting at the MEDEA locus in Arabidopsis. Cold Spring Harb Symp Quant Biol 69:465–475PubMedCrossRefGoogle Scholar
  80. Surzycki SA, Belknap WR (1999) Characterization of repetitive DNA elements in Arabidopsis. J Mol Evol 48:684–691PubMedCrossRefGoogle Scholar
  81. Sweredoski M, DeRose-Wilson L, Gaut BS (2008) A comparative computational analysis of nonautonomous helitron elements between maize and rice. BMC Genomics 9:467PubMedCrossRefGoogle Scholar
  82. Talbert LE, Chandler VL (1988) Characterization of a highly conserved sequence related to mutator transposable elements in maize. Mol Biol Evol 5:519–529PubMedGoogle Scholar
  83. Tempel S, Giraud M, Lavenier D, Lerman IC, Valin AS, Couée I, Amrani AE, Nicolas J (2006) Domain organization within repeated DNA sequences: application to the study of a family of transposable elements. Bioinformatics 22:1948–1954PubMedCrossRefGoogle Scholar
  84. Tempel S, Nicolas J, El Amrani A, Couee I (2007) Model-based identification of Helitrons results in a new classification of their families in Arabidopsis thaliana. Gene 403:18–28PubMedCrossRefGoogle Scholar
  85. The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195CrossRefGoogle Scholar
  86. Tsukamoto T, Hauck NR, Tao R, Jiang N, Iezzoni AF (2010) Molecular and genetic analyses of four nonfunctional S haplotype variants derived from a common ancestral S haplotype identified in sour cherry (Prunus cerasus L.). Genetics 184:411–427PubMedCrossRefGoogle Scholar
  87. Turcotte K, Srinivasan S, Bureau T (2001) Survey of transposable elements from rice genomic sequences. Plant J 25:169–179PubMedCrossRefGoogle Scholar
  88. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604PubMedCrossRefGoogle Scholar
  89. Walbot V, Rudenko GN (2002) MuDR/Mu transposable elements of maize. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM Press, Washington, D.C., pp 533–564Google Scholar
  90. Wang Q, Dooner HK (2006) Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci USA 103:17644–17649PubMedCrossRefGoogle Scholar
  91. Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039PubMedCrossRefGoogle Scholar
  92. Wicker T, Narechania A, Sabot F, Stein J, Vu GT, Graner A, Ware D, Stein N (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982PubMedCrossRefGoogle Scholar
  93. Wicker T, Narechania A, Sabot F, Stein J, Vu GT et al (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9:518PubMedCrossRefGoogle Scholar
  94. Wicker T, Buchmann JP, Keller B (2010) Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Res 20:1229–1237PubMedCrossRefGoogle Scholar
  95. Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue MT, Spillane C, Nordborg M, Rehmsmeier M, Köhler C (2011) High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm. PLoS Genet 7:e1002126PubMedCrossRefGoogle Scholar
  96. Xu JH, Messing J (2006) Maize haplotype with a helitron-amplified cytidine deaminase gene copy. BMC Genet 7:52PubMedCrossRefGoogle Scholar
  97. Yang L, Bennetzen JL (2009a) Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci USA 106:19922–19927PubMedGoogle Scholar
  98. Yang L, Bennetzen JL (2009b) Structure-based discovery and description of plant and animal Helitrons. Proc Natl Acad Sci USA 106:12832–12837PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Waksman InstituteRutgers UniversityPiscatawayUSA
  2. 2.Department of Plant BiologyRutgers UniversityNew BrunswickUSA

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