A new class of rye-specific repetitive DNA elements designated Superior has been identified. The rye genome library was constructed by cleavage with Eco O109I, the recognition sites of which consisted of 5′-PuGGNCCPy-3′ multi-sequences and were present with high frequency in the rye repetitive families. A novel 495-bp segment enriched in the rye genome was successfully identified. Southern blot hybridization and fluorescence in situ hybridization using the repetitive element showed a dispersed array through all 7 chromosomes of rye. The repetitive DNA element did not share identity with known class I or class II transposable elements or known repetitive elements. Only several DNA segments in BACs and ESTs of barley showed partial similarity to the repetitive DNA element in all DNA databases of living species. The new class of dispersed repetitive elements was designated Superior. The entire structure of Superior was determined by using a rye genomic library of lambda FIXII screened by the 495-bp probe. The Superior family consisted of 1,292-bp, 1,324-bp, and 1,432-bp elements in which the 5′ regions had been destroyed, indicating the presence of considerable structural diversity. Superior might be a useful tool for studying genomic organization and differentiation.

Keywords:
Barley EST, Dispersed repetitive sequence family, Eco O109I, Genome-specific DNA element, Rye
1.
Alkhimova OG, Mazurok NA, Potapova TA, Zakian SM, Heslop-Harrison JS, Vershinin AV: Diverse patterns of the tandem repeats organization in rye. Chromosoma 113:42–52 (2004).
2.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 (1997).
3.
Alves E, Ballesteros I, Linacero R, Vazquez AM: RYS1, a foldback transposon, is activated by tissue culture and shows preferential insertion points into the rye genome. Theor Appl Genet 111:431–436 (2005).
4.
Appels R, Dennis ES, Smyth DR, Peacock WJ: Two repeated DNA sequences from the heterochromatic regions of rye (Secale cereale) chromosomes. Chromosoma 84:265–277 (1981).
5.
Appels R, Gustafson JP, May CE: Structural variation in the heterochromatin of rye chromosomes in Triticales. Theor Appl Genet 63:235–244 (1982).
6.
Appels R, Moran LB, Gustafson JP: 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 (1986).
7.
Arumuganathan K, Earle ED: Nuclear DNA content of some important plant species. Plant Mol Biol Report 9:211–215 (1991).
8.
Barakat A, Carels N, Bernardi G: The distribution of genes in the genomes of Gramineae. Proc Natl Acad Sci USA 94:6857–6861 (1997).
9.
Bedbrook JR, Jones J, O’Dell M, Thompson RD, Flavell RB: A molecular description of telomeric heterochromatin in Secale species.Cell 19:545–560 (1980).
10.
Bennett MD, Leitch IJ: Nuclear DNA amounts in angiosperms. Ann Bot 76:113–176 (1995).
11.
Bennetzen JL: Transposable element contribution to plant gene and genome evolution. Plant Mol Biol 42:251–269 (2000).
12.
Bennetzen JL, Ma J, Devos KM: Mechanisms of recent genome size variation in flowering plants. Ann Bot 95:127–132 (2005).
13.
Brown JWS, Marshall DF, Echeverria M: Intronic noncoding RNAs and splicing. Trends Plant Sci 13:335–342 (2008).
14.
Cuadrado A, Jouve M: Distribution of highly repeated DNA sequences in species of the genus Secale. Genome 40:309–317 (1997).
15.
Cuadrado A, Jouve M: Evolutionary trends of different repetitive DNA sequences during speciation in the genus Secale.J Hered 93:339–345 (2002).
16.
Cuadrado A, Ceoloni C, Jouve M: Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization. Genome 38:1061–1069 (1995).
17.
Cuadrado A, Vitellozzi F, Jouve M, Ceoloni C: Fluorescence in situ hybridization with multiple repeated DNA probes applied to the analysis of wheat-rye chromosome pairing. Theor Appl Genet 94:347–355 (1997).
18.
Doolittle WF, Sapienza C: Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601–603 (1980).
19.
Feschotte C: Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9:397–405 (2008).
20.
Feschotte C, Wessler SR: Mariner-like transposases are widespread and diverse in flowering plants. Proc Natl Acad Sci USA 99:280–285 (2002).
21.
Flavell AJ, Dumbar E, Anderson R, Pearce SR, Hartley R, Kumar A: Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acid Res 20:3639–3644 (1992).
22.
Flavell AJ, Pearce SR, Kumar A: Plant transposable elements and the genome. Curr Opin Genet Dev 4:838–844 (1994).
23.
Flavell RB, Smith DB: Nucleotide organization in the wheat genome. Heredity 37:231–252 (1976).
24.
Flavell RB, Bennett MD, Smith JB, Smith DB: Genome size and the proportion of repeated sequence DNA in plants. Biochem Genet 12:257–269 (1974).
25.
Flavell RB, Rimpau JR, Smith DB: Repeated sequence DNA relationships in four cereal genomes. Chromosoma 63:205–222 (1977).
26.
Flavell RB, O’Dell M, Hutchinson J: Nucleotide sequence organization in plant chromosomes and evidence for sequence translocation during evolution. Cold Spring Harbor Symp Quant Biol 45:501–506 (1981).
27.
Francki MG: Identification of Bilby, a diverged centromeric Ty1-copia retrotransposon family from cereal rye (Secale cereale L.). Genome 44:266–274 (2001).
28.
Francki MG, Crasta OR, Sharma HC, Ohm HW, Anderson JM: Structural organization of an alien Thinopyrum intermedium group 7 chromosome in U.S. soft red winter wheat (Triticum aestivum L.). Genome 40:716–722 (1997).
29.
Graybosch RA: Uneasy unions: quality effects of rye chromatin transfers to wheat. J Cereal Sci 33:3–16 (2001).
30.
Guidet F, Rogowsky PM, Taylor C, Song W, Langridge P: Cloning and characterization of a new rye-specific repeated sequence. Genome 34:81–87 (1991).
31.
He M, Wild A, Kaderbhai MA: A simple single-step procedure for small-scale preparation of Escherichia coli plasmids. Nucleic Acids Res 18:1660 (1989).
32.
Heslop-Harrison JS, Brandes A, Taketa S, Schmidt T, Vershinin AV, et al: The chromosomal distribution of Ty1-copia group retrotransposable elements in higher plants and their implication for genome evolution. Genetica 100:197–204 (1997).
33.
Kim JM, Vanguri S, Boeke JD, Gabriel A, Voyats DF: Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8:464–478 (1998).
34.
Korzun V, Balzer HJ, Balzer A, Bäumlein H, Börner A: Chromosomal location of three wheat sequences with homology to pollen allergen encoding, DNA replication regulating, and DNA (cytosine-5)-methyltransferase genes in wheat and rye. Genome 39:1213–1215 (1996).
35.
Kumar A: The adventures of the Ty1-copia group of retrotransposons in plants. Trends Genet 12:41–43 (1996).
36.
Kumar A, Pearce SR, McLean K, Harrison GE, Heslop-Harrison JS, et al: The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers. Genetica 100:205–217 (1997).
37.
Langdon T, Jenkins G, Hasterok R, Jones RN, King IP: A high-copy-number CACTA family transposon in temperate grasses and cereal. Genetics 163:1097–1108 (2003).
38.
Lapitan NLV, Sear RG, Rayburn AL, Gill BS: Detection of chromosome breakpoints by in situ hybridization with a biotin-labeled DNA probe. J Hered 77:415–419 (1986).
39.
Lima-Brito L, Guedes-Pinto H, Harrison GE, Heslop-Harrison JS: Molecular cytogenetic analysis of durum wheat×tritordeum hybrids. Genome 40:362–369 (1997).
40.
Marillonnet S, Wessler SR: Extreme structural heterogeneity among the members of maize. Genetics 150:1245–1246 (1998).
41.
McGookin R: RNA extraction by the guanidine thiocyanate procedure, in Walker JM (ed): Methods in Molecular Biology Vol. 2 Nucleic Acids, pp 113–116 (Humana Press, Clifton 1984).
42.
McIntyre CL, Clarke BC, Appels R: Amplification and dispersion of repeated DNA sequences in the Triticeae. Plant Syst Evol 160:39–59 (1988).
43.
McIntyre CL, Pereira S, Moran LB, Appels R: New Secale cereale (rye) DNA derivatives for the detection of rye chromosome segments in wheat. Genome 33:635–640 (1990).
44.
Murata S, Takasaki N, Saitou M, Okada N: Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc Natl Acad Sci USA 90:6995–6999 (1993).
45.
Myers BC, Tingey SV, Morgante M: Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11:1660–1676 (2001).
46.
Nagy ED, Lelley T: Genetic and physical mapping of sequence-specific amplified polymorphic (SSAP) markers on the 1RS chromosome arm of rye in a wheat background. Theor Appl Genet 107:1271–1277 (2003).
47.
Ohshima K, Hamada M, Terai Y, Okada N: The 3′ ends of tRNA-derived short interspersed repetitive elements are derived from the 3′ ends of long interspersed repetitive elements. Mol Cell Biol 16:3756–3764 (1996).
48.
Okada N: SINEs: short interspersed repeated elements of the eukaryotic genome. Trends Ecol Evol 6:358–361 (1991).
49.
Orgel LE, Crick FHC: Selfish DNA: the ultimate parasite. Nature 284:604–607 (1980).
50.
Park ET, Kazazian HH Jr: Mobile elements and the human genome. Nat Rev Genet1:134–144 (2000).
51.
Pearce SR, Harrison GE, Heslop-Harrison JS, Flavell AJ, Kumar A: Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale careale). Genome 40:617–625 (1997).
52.
Ramakrishna W, Dubcovsky J, Park YJ, Busso C, Emberton J, et al: Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162:1389–1400 (2002).
53.
Rogowsky PM, Manning S, Liu JY, Langridge P: The R173 family of rye-specific repetitive DNA sequences: a structural analysis. Genome 34:88–95 (1991).
54.
Rogowsky PM, Liu JY, Manning S, Taylor C, Langridge P: Structural heterogeneity in the R173 family of rye-specific repetitive DNA sequences. Plant Mol Biol 20:95–102 (1992).
55.
SanMiguel P, Bennetzen JL: Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann Bot 82:37–44 (1998).
56.
SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, et al: Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765–768 (1996).
57.
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL: The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45 (1998).
58.
Siomi H, Siomi MC: Interactions between transposable elements and Argonautes have (probably) been shaping the Drosophila genome throughout evolution. Curr Opin Genet Dev 18:181–187 (2008).
59.
Smith DB, Flavell RB: Nucleotide sequence organization in the rye genome. Biochim Biophys Acta 474:82–97 (1977).
60.
Stein N: Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosome Res15:21–31 (2007).
61.
Suoniemi A, Anamthawat-Jonsson K, Arna T, Schulman AH: Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome. Plant Mol Biol 30:1321–1329 (1996).
62.
Tabei Y, Tsuda K, Kin T, Asai K: SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinformatics 22:1723–1729 (2006).
63.
Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, Bennetzen JL, Avramova Z: Colinearity and its exceptions on orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 96:7409–7414 (1999).
64.
Tomita M: Revolver-2: a novel transposon-like element from rye. United States Patent No. 7,351,536B2 (2008).
65.
Tomita M, Shinohara K, Morimoto M: Revolver is a new class of transposon-like gene composing the Triticeae genome. DNA Res 15:49–62 (2008).
66.
Tomita M, Akai K, Morimoto T: Genomic subtraction recovers rye-specific DNA elements enriched in the rye genome. Mol Biotechnol 42:160–167 (2009).
67.
Vershinin AV, Schwarzacher T, Heslop-Harrison JS: The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes. Plant Cell 7:1823–1833 (1995).
68.
Vershinin AV, Alkhimova OG, Heslop-Harrison JS: Molecular diversification of tandemly organized DNA sequences and heterochromatic chromosome regions in some Triticeae species. Chromosome Res 4:517–525 (1996).
69.
Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav A, et al: Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11:1769–1784 (1999).
70.
Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, et al: Genetic distribution of Bare-1 like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687–694 (1997).
71.
Wendel JF: Genome evolution in polyploids. Plant Mol Biol 42:225–249 (2000).
72.
Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, Keller B: Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J 26:307–316 (2001).
73.
Wicker T, Guyot R, Yahiaoui N, Keller B: CACTA transposons in Triticeae: a diverse family of high-copy repetitive elements. Plant Physiol 132:52–63 (2003).
74.
Wicker T, Narechania A, Sabot F, Stein J, Vu GTH, et al: Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9:518 (2008).
75.
Yuan WY, Tomita M: Centromeric distribution of 350-family in Dasypyrum villosum and its application to identifying Dasypyrum chromatin in the wheat genome. Hereditas 146:58–66 (2009).
76.
Zeller FJ, Fischbec G: Cytologische Untersuchungen zur Identifizierung des Fremdchromosoms in derWeizensorte Zorba (W565). Z Pflanzenzuchtg 66:260–265 (1971).
77.
Zhang X, Jiang N, Feschotte C, Wessler SR: PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements.Genetics 166:971–986 (2004).
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