Revolver is a new class of transposon-like gene composing the Triticeae genome

DNA Research

Volumn 15, Issue 1, 2008, Pages 49-62

  Tomita, Motonori ^a   Shinohara, Kasumi ^a   Morimoto, Mayu ^a  

^a TOTTORI UNIVERSITY   (Japan)

Author keywords

Genomic component; Structural and quantitative divergence; Transcript; Transposon like gene

Indexed keywords

AMINO ACID; COMPLEMENTARY DNA;

ARTICLE; DNA DETERMINATION; DNA SEQUENCE; EXON; GENE DELETION; GENE ISOLATION; GENE STRUCTURE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; INTRON; MOLECULAR CLONING; MOLECULAR PROBE; NONHUMAN; PLANT CHROMOSOME; PLANT EVOLUTION; PLANT GENE; PLANT GENOME; PLANT PRODUCT; REVOLVER GENE; RYE; SCREENING; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION; TRANSPOSON; TRITICEAE; WHEAT; AMINO ACID SEQUENCE; GENETICS; GENOME; MOLECULAR GENETICS;

SECALE CEREALE; TRITICEAE; TRITICUM AESTIVUM;

AMINO ACID SEQUENCE; DNA TRANSPOSABLE ELEMENTS; GENOME, PLANT; INTRONS; MOLECULAR SEQUENCE DATA; SECALE CEREALE; TRITICUM;

EID: 48249109113     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsm029     Document Type: Article

References (83)

1. Flavell, R. B., Rimpau, J. R. and Smith, D. B. 1977, Repeated sequence DNA relationships in four cereal genomes, Chromosoma, 63, 205-222.
2. Grandbastien, M. A. 1992 Retroelements in higher plants, Trends Genet, 8, 103-108.
3. Barakat, A., Carels, N. and Bernardi, G. 1997, The distribution of genes in the genomes of Gramineae, Proc. Natl. Acad. Sci. USA, 94, 6857-6861.
4. Panstruga, R., Buschges, R., Piffanelli, P. and Schulze-Lefert, P. 1998, A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome, Nucleic Acids Res., 26, 1056-1062.
5. Park, E. T. and Kazazian, H. H. Jr. 2000, Mobile elements and the human genome, Nat. Rev. Genet., 1, 134-144.
6. SanMiguel, P. and Bennetzen, J. L. 1998, Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons, Ann. Bot., 82, 37-44.
7. Myers, B. C., Tingey, S.V. and Morgante, M. 2001, Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome, Genome Res., 11, 1660-1676.
8. Finnegan, D. J. 1992, Transposable elements, Curr. Opin. Genet. Dev., 2, 861 -867.
9. Boeke, J. D. and Chapman, K. B. 1991, Retrotransposition mechanisms, Cuur. Opin. Cell Biol., 3, 502-507.
10. Adams, S. E., Mellor, J., Gull, K., Sim, R. B., Tuite, M. F., Kingsman, S. M. and Kingsman, A. J. 1987, The function and relationships of Ty-VLP proteins in yeast reflect those of mammalian retroviral proteins, Cell, 49, 111-119.
11. Doolittle, R. F., Feng, D.-F., Johnson, M. S. and McClure, M. A. 1989, Origins and evolutionary relationships of retroviruses, Quant. Rev. Biol., 64, 1-30.
12. Flavell, A. J., Dunbar, E., Anderson, R., Pearce, S. R., Hartley, R. and Kumar, A. 1992, Ty1 -copia group retrotransposons are ubiquitous and heterogeneous in higher plants, Nucleic Acids Res., 20, 3639-3644.
13. Voytas, D. F., Cummings, M. P., Konieczny, A. K., Ausubel, F. M. and Rodermel, S. R. 1992, Copia-like retrotransposons are ubiquitous among plant, Proc. Natl. Acad. Sci. USA, 89, 7124-7128.
14. Bennetzen, J. L 1996, The Mutator transposable element system of maize, Curr. Top. Microbiol. Immunol., 204, 195-229.
15. Suoniemi, A., Tanskanen, J. and Schulman, A. H. 1998, Gypsy-like retrotransposons are widespread in the plant kingdom, Plant J., 13, 699-705.
16. Vicient, C. M., Kalendar, R. and Schulman, A. H. 2001, Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants, Genome Res., 11, 2041 -2049.
17. Bennetzen, J. L. 2000, Transposable element contribution to plant gene and genome evolution, Plant Mol. Biol., 42, 251 -269.
18. Bennetzen, J. L., Ma, J. and Devos, K. M. 2005, Mechanisms of recent genome size variation in flowering plants, Annals Botany, 95, 127-132.
19. Flavell, A. J., Pearce, S. R. and Kumar, A. 1994, Plant transposable elements and the genome, Curr. Opin. Genet. Dev., 4, 838-844.
20. Kunze, R. and Well, C. F. 2002, The hAT and CACTA superfamilies of plant transposons, In: Craig, N. L., Craigie, R., Gellert, M. and Lambowitz, M.(eds.), Mobile DNA II, Washington, DC: American Society of Microbiology, 565-610.
21. Zhang, X., Jiang, N., Feschotte, C. and Wessler, S. R. 2004, PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements, Genetics, 166, 971-986.
22. Wessler, S. R., Bureau, T. E. and White, S.E. 1995, LTR-retrotransposons and MITEs: Important players in the evolution of plant genomes, Curr. Opin. Genet. Dev., 5, 814-821.
23. Feschotte, C. and Wessler, S. R. 2002, Mariner-like transposases are widespread and diverse in flowering plants, Proc. Natl. Acad. Sci. USA, 99, 280-285.
24. Von Strenberg, R. M., Novick, G. E., Gao, G-P. and Herrera, R. J. 1993, Genome canalization: the coevolution of transposable and interspersed repititive elements with single copy DNA, In: McDonald, J. F.(ed.), Transposable Elements and Evolution, Dordrecht Kluwer Academic Publishers, 108-139.
25. Marillonnet, S. and Wessler, S. R. 1998, Extreme structural heterogeneity among the members of a maize, Genetics, 150, 1245-1246.
26. SanMiguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y. and Bennetzen, J. L 1998, The paleontology of intergene retrotransposons of maize, Nature Genet., 20:43-45.
27. Kumar, A., Pearce, S. R., McLean, K., Harrison, G., HeslopHarrison, J. S., Waugh, R. and Flavell, A. J. 1997, The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers, Genetica, 100, 205-217.
28. Hirochika, H., Sugimoto, K., Otsuki, Y., Tsugawa, H. and Kanda, M. 1996, Retrotransposons of rice involved in mutations induced by tissue culture, Proc. Natl. Acad. Sci. USA, 93, 7783-7788.
29. Bennetzen, J. L. 1996, The contribution of retroelements to plant genome organization, function and evolution, Trends Microbiol., 4, 347-353.
30. Flavell, R. B., Bennett, M. D., Smith, J. B. and Smith, D. B. 1974, Genome size and the proportion of repeated sequence DNA in plants, Biochem. Genet., 12, 257-269.
31. Guidet, F., Rogowsky, P., Taylor, C., Song, W. and Langridge, P. 1991, Cloning and characterization of a new rye-specific repeated sequence, Genome, 34, 81-87.
32. Cuadrado, A., Vitellozzi, F., Jouve, N. and Ceoloni, C. 1997, Fluorescence in situ hybridization with multiple repeated DNA probes applied to the analysis of wheat-rye chromosome pairing, Theor. Appl. Genet., 94, 347-355.
33. Bedbrook, J. R., Jones, J., O'Dell, M., Thompson, R. D. and Flavell, R. B. 1980, A molecular description of telomeric heterochromatin in Secale species, Cell, 19, 545-560.
34. Appels, R., Dennis, E. S., Smyth, D. R. and Peacock, W. J. 1981, Two repeated DNA sequences from the heterochromatic regions of rye (Secale cereale) chromosomes, Chromosoma, 84, 265-277.
35. Appels, R., Moran, L. B. and Gustafson, J. P. 1986, Rye heterochromatin. I. Studies on clusters of the major repeating sequence and the identification of a new dispersed repetitive sequence element, Can. J. Genet. Cytol., 28, 645-657.
36. Lamar, E. E. and Palmer, E. 1984, Y-encoded, species-specific DNA in mice: evidence that the Y chromosome exists in two polymorphic forms in inbred strains, Cell, 37, 171-177.
37. Heslop-Harrison, J.S, Brandes, A., Taketa, S., Schmidt, T., Vershinin, A. V., Alkhimova, E. G., Kamm, A., Doudrick, R., Schwarzacher, T., Katsiotis, A., et al. 1997, The chromosomal distribution of Ty1-copia group retrotransposable elements in higher plants and their implication for genome evolution, Genetica, 100, 197-204.
38. Rogowsky, P. M., Manning, S., Liu, J. Y. and Langridge, P. 1991, The R173 family of rye-specific repetitive DNA sequences: a structural analysis, Genome, 34, 88-95.
39. Rogowsky, P. M., Liu, J. Y., Manning, S., Taylor, C. and Langridge, P. 1992, Structural heterogeneity in the R173 family of rye-specific repetitive DNA sequences, Plant Mol. Biol., 20, 95-102.
40. McIntyre, C. L., Pereira, S., Moran, L. B. and Appels, R. 1990, New Secale cereale (rye) DNA derivatives for the detection of rye chromosome segments in wheat, Genome, 33, 635-640.
41. Vershinin, A. V., Schwarzacher, T. and Heslop-Harrison, J. S. 1995, The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes, Plant Cell, 7, 1823-1833.
42. Manninen, I. and Schulman, A. H. 1993, BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.), Plant Mol. Biol., 22, 829-846.
43. Suoniemi, A., Anamthawat-Jonsson, K., Arna, T. and Schulman, A. H. 1996, Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L) genome, Plant Mol. Biol., 30, 1321 -1329.
44. Suoniemi, A., Narvanto, A. and Schulman, A. H. 1996, The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays, Plant Mol. Biol., 31, 295-306.
45. Vicient, C. M., Suoniemi, A., Anamthawat-Jonsson, K., Tanskanen, J., Beharav, A., Nevo, E. and Schulman, A. H. 1999, Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum, Plant Cell, 11, 1769-1784.
46. Kalendar, R., Vicient, C. M., Peleg, O., AnamthawatJonsson, K., Bolshoy, A. and Schulman, A. H. 2004, Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes, Genetics, 166, 1437-1450.
47. Shirasu, K., Schulman, A. H., Lahaye, T. and Schuze-Lefert, P. 2000, A contiguous 66 kb barley DNA sequence provides evidence for reversible genome expansion, Genome Res., 10, 908-915.
48. Grandbastien, M. A. 1998, Activation of plant retrotransposons under stress conditions, Trends Plant Sci., 3, 181-187.
49. Kumar, A. and Bennetzen, J. L. 1999, Plant retrotransposons, Annu. Rev. Genet., 33, 479-532.
50. Vernhettes, S., Grandbastien, M.-A. and Casacuberta, J. M. 1997, In vivo characterization of transcriptional regulatory sequences involved in the defence-associated expression of the tobacco retrotransposon Tnt1, Plant Mol. Biol., 35, 673-679.
51. Takeda, S., Sugimoto, K., Otsuki, H. and Hirochika, H. 1998, Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate, Plant Mol. Biol., 36, 365-376.
52. Hirochika, H. 1993, Activation of tobacco retrotransposons during tissue culture, EMBO J., 12, 2521-2528.
53. Ostertag, E. M. and Kazazian, H. H. Jr. 2001, Biology of mammalian L1 retrotransposons, Annu. Rev. Genet., 35, 501-538.
54. Hamilton, A., Voinnet, O., Chappell, L. and Baulcombe, D. 2002, Two classes of short interfering RNA in RNA silencing, EMBO J., 21, 4671 -4679.
55. Llave, C., Kasschau, K. D., Rector, M. A. and Carrington, J. C. 2002, Endogenous and silencing-associated small RNAs in plants, Plant Cell, 14, 1605-1619.
56. Sunker, R., Girke, T. and Zhu, J-K. 2005, Identification and characterization of endogenous small interfering RNAs from rice, Nucleic Acids Res., 33, 4443-4454.
57. Bennett, M. D. and Leitch, I. J. 1995, Nuclear DNA amounts in angiosperms, Ann. Bot., 76, 113-176.
58. Thomas, C. A. 1971, The genetic organization of chromosomes, Annu. Rev. Genet., 5, 237-256.
59. Arumuganathan, K. and Earle, E. D. 1991, Nuclear DNA content of some important plant species, Plant Mol. Biol. Reporter 9, 208-218.
60. Doolittle, W. F. and Sapienza, C. 1980, Selfish genes, the phenotype paradigm and genome evolution, Nature, 284, 601-603.
61. Orgel, L. E. and Crick, F. H. C. 1980, Selfish DNA: the ultimate parasite, Nature, 284, 604-607.
62. Wicker, T., Stein, N., Albar, L., Feuillet, C., Schlagenhauf, E. and Keller, B. 2001, Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution, Plant J., 26, 307-316.
63. SanMiguel, P., Tikhonov, A., Jin, Y. K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P. S., Edwards, K. J., Lee, M., Avramova, Z., et al. 1996, Nested retrotransposons in the intergenic regions of the maize genome, Science, 274, 765-768.
64. Tikhonov, A. P., SanMiguel, P. J., Nakajima, Y., Gorensten, N. M., Bennetzen, J. L. and Avramova, Z. 1999, Colinearity and its exceptions on orthologous adh regions of maize and sorghum, Proc. Natl. Acad. Sci. USA, 96, 7409-7414.
65. Kim, J. M., Vanguri, S., Boeke, J. D., Gabriel, A. and Voytas, D. F. 1998, Transpossble elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence, Genome Res., 8, 464-478.
66. Ramakrishna, W., Dubcovsky, J., Park, Y.-J., Busso, C., Emberton, J., SanMiguel, P. and Bennetzen, J.L. 2002, Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes, Genetics, 162, 1389-1400.
67. Wicker, T., Guyot, R., Yahiaoui, N. and Keller, B. 2003, CACTA transposons in Triticeae: a diverse family of high-copy repetitive elements, Plant Physiol., 132, 52-63.
68. Langdon, T., Jenkins, G., Hasterok, R., Jones, R. N. and King, I. P. 2003, A high-copy-number CACTA family transposon in temperate grasses and cereal, Genetics, 163, 1097-1108.
69. Dvorak, J., McGuire, P. E. and Cassidy, B. 1988, Apparent sources of the A genomes of wheats inferred from polymorphism in abundance and restriction fragment length of repeated nucleotide sequences, Genome, 30, 680-689.
70. Dvorak, J. and Zhang, H. B. 1992, Reconstruction of the phylogeny of the genus Triticum from variation in repeated nucleotide sequences, Theor. Appl. Genet., 84, 419-429.
71. Friebe, B. and Gill, B. S. 1996, Chromosome banding and genome analysis in diploid and cultivated polyploid wheats, In: Jauhar, P. P.(ed.), Methods of Genome Analysis in Plants, Boca Raton, FL, NY: CRC Press, 39-60.
72. Tsunewaki, K. 1996, Plasmon analysis as the counter-part of genome analysis, In: Jauhar, P. P.(ed.), Methods of Genome Analysis in Plants, Boca Raton, FL, NY: CRC Press, 271-299.
73. Feldman, M., Lupton, F. G. H. and Miller, T. E. 1995, Wheats, In: Smartt, J. and Simmonds, N. W(eds.), Evolution of Crops, 2nd Ed., London: Longman Scientific, 184-192.
74. Leitch, I. J. and Bennett, M. D. 1997, Polyploidy in angiosperms, Trends Plant Sci., 2, 470-476.
75. Wendel, J. F. 2000, Genome evolution in ployploids, Plant Mol. Biol., 42, 225-249.
76. Feldman, M., Liu, B., Segal, G., Abbo, S., Levy, A. A. and Vega, J. M. 1997, Rapid elimination of low-copy DNA sequence in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes, Genetics, 147, 1381 -1387.
77. Ozkan, H., Levy, A. A. and Feldman, M. 2001, Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group, Plant Cell, 13, 1735-1747.
78. SanMiguel, P., Remakrishna, W., Bennetzen, J. L., Busso, C. and Dubcovsky, J. 2002, Transposable elements, genes and recombination in a 215 kb contig from wheat chromosome 5Am, Funct. Integr. Genomics, 2, 70-80.
79. Bennetzen, J. L. and Kellogg, E. A. 1997, Do plants have a one-way ticket to genomic obesity? Plant Cell, 9, 1509-1514.
80. Kellogg, E. A. 1998, Relationships of cereal crops and other grasses, Proc. Natl. Acad. Sci. USA, 95, 2005-2010.
81. Leitch, I. J., Chase, M. W. and Bennett, M. D. 1998, Phylogenetic analysis of DNAC-value provides evidence for a small ancestral genome size in flowering plants, Annal. Bot., 82, 85-94.
82. Petrov, D. A., Sangster, T. A., Johnston, J. S., Hartl, D. L. and Shaw, K. L. 2000, Evidence for DNA loss as a determinant of genome size, Science, 287, 1060-1062.
83. Tomita, M. 2005, Revolver-2: a novel transposon-like element from rye, United States Patent and Trademark Office, Published Application No. 20050091710.