Genomic subtraction recovers rye-specific DNA elements enriched in the rye genome

Molecular Biotechnology

Volumn 42, Issue 2, 2009, Pages 160-167

  Tomita, Motonori ^a   Akai, Keiichi ^a   Morimoto, Takayoshi ^a  

^a TOTTORI UNIVERSITY   (Japan)

Author keywords

Genome specific DNA elements; Genomic subtraction; Repetitive sequence family; Rye

Indexed keywords

GENOME-SPECIFIC DNA ELEMENTS; GENOMIC DNA; GENOMIC ORGANIZATION; GENOMIC SUBTRACTION; HIGH FREQUENCY; MULTI-SEQUENCES; MULTIMERS; RECOGNITION SITE; REPETITIVE-SEQUENCE FAMILY; RESTRICTION ENZYMES; RYE; SOUTHERN BLOT HYBRIDIZATION; SUBTRACTION METHOD;

ALKYLATION; DNA; DNA SEQUENCES; ENZYMES; METHYLATION; NUCLEIC ACIDS;

GENES;

PLANT DNA;

ARTICLE; CHROMOSOME; DNA HYBRIDIZATION; DNA METHYLATION; DNA SEQUENCE; MBOI GENE; NONHUMAN; PLANT GENE; PLANT GENOME; PSTI GENE; RYE; SALI GENE; SOUTHERN BLOTTING; TELOMERE; GENETICS; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE REPEAT;

SECALE CEREALE; TRITICUM AESTIVUM;

DNA, PLANT; GENOME, PLANT; NUCLEIC ACID HYBRIDIZATION; REPETITIVE SEQUENCES, NUCLEIC ACID; SECALE CEREALE;

EID: 69249229876     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12033-009-9151-2     Document Type: Article

References (47)

1. OG Alkhimova NA Mazurok TA Potapova SM Zakian JS Heslop-Harrison AV Vershinin 2004 Diverse patterns of the tandem repeats organization in rye Chromosoma 113 42 52 10.1007/s00412-004-0294-4 10.1007/s00412-004-0294-4 1:CAS:528:DC%2BD2cXmt1Kksb0%3D (Pubitemid 39236721)
2. E Alves I Ballesteros R Linacero AM Vazquez 2005 RYS1, a foldback transposon, is activated by tissue culture and shows preferential insertion points into the rye genome Theoretical and Applied Genetics 111 431 436 10.1007/s00122-005-2013-9 10.1007/s00122-005-2013-9 1:CAS:528: DC%2BD2MXovVKktLo%3D (Pubitemid 41204226)
3. R Appels ES Dennis DR Smyth WJ Peacock 1981 Two repeated DNA sequences from the heterochromatic regions of rye (Secale careale) chromosomes Chromosoma 84 265 277 10.1007/BF00399137 10.1007/BF00399137 1:CAS:528:DyaL38XmtlKjuw%3D%3D
4. R Appels JP Gustafson CE May 1982 Structural variation in the heterochromatin of rye chromosomes in Triticales Theoretical and Applied Genetics 63 235 244 10.1007/BF00304002 10.1007/BF00304002
5. R Appels LB Moran JP Gustafson 1986 Rye heterochromatin. I. Studies on clusters of the major repeating sequence and the identification of a new dispersed repetitive sequence element Canadian Journal of Genetics and Cytology 28 645 657 1:CAS:528:DyaL2sXivVClsA%3D%3D
6. JR Bedbrook J Jones M O'Dell RD Thompson RB Flavell 1980 A molecular description of telomeric heterochromatin in Secale species Cell 19 545 560 10.1016/0092-8674(80)90529-2 10.1016/0092-8674(80)90529-2 1:CAS:528: DyaL3cXhsVentr8%3D
7. JL Bennetzen J Ma KM Devos 2005 Mechanisms of recent genome size variation in flowering plants Annals of Botany 95 127 132 10.1093/aob/mci008 10.1093/aob/mci008 1:CAS:528:DC%2BD2MXht1Kiurw%3D (Pubitemid 41214455)
8. JWS Brown DF Marshall M Echeverria 2008 Intronic noncoding RNAs and splicing Trends in Plant Science 13 335 342 10.1016/j.tplants.2008.04.010 10.1016/j.tplants.2008.04.010 1:CAS:528:DC%2BD1cXotlOjt7o%3D
9. A Cuadrado C Ceoloni M Jouve 1995 Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization Genome 38 1061 1069 10.1139/g95-101 10.1139/g95-101 1:CAS:528:DyaK28XptlWjsA%3D%3D
10. A Cuadrado M Jouve 1997 Distribution of highly repeated DNA sequences in species of the genus Secale Genome 40 309 317 10.1139/g97-043 10.1139/g97-043 1:CAS:528:DyaK2sXksFGkur8%3D
11. A Cuadrado M Jouve 2002 Evolutionary trends of different repetitive DNA sequences during speciation in the genus Secale The Journal of Heredity 93 339 345 10.1093/jhered/93.5.339 10.1093/jhered/93.5.339 1:CAS:528: DC%2BD3sXhtFyku70%3D (Pubitemid 36083968)
12. A Cuadrado F Vitellozzi M Jouve C Ceoloni 1997 Fluorescence in situ hybridization with multiple repeated DNA probes applied to the analysis of wheat-rye chromosome pairing Theoretical and Applied Genetics 94 347 355 10.1007/s001220050422 10.1007/s001220050422 1:CAS:528:DyaK2sXivVakurc%3D (Pubitemid 27164895)
13. RB Flavell MD Bennett JB Smith DB Smith 1974 Genome size and the proportion of repeated sequence DNA in plants Biochemical Genetics 12 257 269 10.1007/BF00485947 10.1007/BF00485947 1:CAS:528:DyaE2MXntVeguw%3D%3D
14. AJ Flavell E Dumbar R Anderson SR Pearce R Hartley A Kumar 1992 Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants Nucleic Acids Research 20 3639 3644 10.1093/nar/20.14.3639 10.1093/nar/20.14. 3639 1:CAS:528:DyaK38XlsVClsbc%3D
15. RB Flavell M O'Dell J Hutchinson 1981 Nucleotide sequence organization in plant chromosomes and evidence for sequence translocation during evolution Cold Spring Harbor Symposia on Quantitative Biology 45 501 506 1:CAS:528: DyaL38XhtFKku7Y%3D
16. AJ Flavell SR Pearce A Kumar 1994 Plant transposable elements and the genome Current Opinion in Genetics and Development 4 838 844 10.1016/0959-437X(94)90068-X 10.1016/0959-437X(94)90068-X 1:CAS:528: DyaK2MXivFKmsrs%3D
17. RB Flavell JR Rimpau DB Smith 1977 Repeated sequence DNA relationships in four cereal genomes Chromosoma 63 205 222 10.1007/BF00327450 10.1007/BF00327450 1:CAS:528:DyaE1cXjt1Sg (Pubitemid 8189388)
18. RB Flavell DB Smith 1976 Nucleotide organization in the wheat genome Heredity 37 231 252 10.1038/hdy.1976.85 10.1038/hdy.1976.85
19. MG Francki 2001 Identification of Bilby, a diverged centromeric Ty1-copia retrotransposon family from cereal rye (Secale cereale L) Genome 44 266 274 10.1139/gen-44-2-266 10.1139/gen-44-2-266 1:CAS:528:DC%2BD3MXjs1Srurk%3D (Pubitemid 32333541)
20. MG Francki OR Crasta HC Sharma HW Ohm JM Anderson 1997 Structural organization of an alien Thinopyrum intermedium group 7 chromosome in U. S. soft red winter wheat (Triticum aestivum L.) Genome 40 716 722 10.1139/g97-794 10.1139/g97-794 1:CAS:528:DyaK2sXntlSnsL0%3D
21. RA Graybosch 2001 Uneasy unions: Quality effects of rye chromatin transfers to wheat Journal of Cereal Science 33 3 16 10.1006/jcrs.2000.0336 10.1006/jcrs.2000.0336 1:CAS:528:DC%2BD3MXlt1Oksw%3D%3D (Pubitemid 32139788)
22. F Guidet PM Rogowsky C Taylor W Song P Langridge 1991 Cloning and characterization of a new rye-specific repeated sequence Genome 34 81 87
23. M He A Wild MA Kaderbhai 1989 A simple single-step procedure for small-scale preparation of Escherichia coli plasmids Nucleic Acids Research 18 1660 10.1093/nar/18.6.1660 10.1093/nar/18.6.1660
24. JS Heslop-Harrison A Brandes S Taketa T Schmidt AV Vershinin EG Alkhimova A Kamm R Doudrick T Schwarzacher A Katsiotis S Kubis A Kumar SR Pearce AJ Flavell GE Harrison 1997 The chromosomal distribution of Ty1-copia group retrotransposable elements in higher plants and their implication for genome evolution Genetica 100 197 204 10.1023/A:1018337831039 10.1023/A:1018337831039 1:CAS:528:DyaK1cXkslWltw%3D%3D
25. M Koenen 1989 Recovery of DNA from agarose gels using liquid nitrogen Trends in Genetics 5 137 1:STN:280:DyaL1Mzjt1yhsg%3D%3D
26. A Kumar 1996 The adventures of the Ty1-copia group of retrotransposons in plants Trends in Genetics 12 41 43 10.1016/0168-9525(96)81393-X 10.1016/0168-9525(96)81393-X 1:CAS:528:DyaK28XhtFagtLk%3D
27. A Kumar SR Pearce K McLean G Harrison JS Heslop-Harrison R Waugh AJ Flavell 1997 The Ty1-copia group of retrotransposons in plants: Genomic organisation, evolution, and use as molecular markers Genetica 100 205 217 10.1023/A:1018393931948 10.1023/A:1018393931948 1:CAS:528:DyaK1cXkslWltA%3D%3D
28. EE Lamar E Palmer 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 10.1016/0092-8674(84)90312-X 10.1016/0092-8674(84)90312-X 1:CAS:528:DyaL2cXksV2ms7s%3D
29. NLV Lapitan RG Sear AL Rayburn BS Gill 1986 Detection of chromosome breakpoints by in situ hybridization with a biotin-labeled DNA probe The Journal of Heredity 77 415 419
30. L Lima-Brito H Guedes-Pinto GE Harrison JS Heslop-Harrison 1997 Molecular cytogenetic analysis of durum wheat×triordeum hybrids Genome 40 362 369 10.1139/g97-049 10.1139/g97-049 1:CAS:528:DyaK2sXksFGkurk%3D
31. N Lisitsyn N Lisitsyn M Wigler 1993 Cloning the differences between two complex genomes Science 259 946 951 10.1126/science.8438152 10.1126/science. 8438152 1:CAS:528:DyaK3sXhsVSrsLY%3D
32. I Manninen AH Schulman 1993 BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.) Plant Molecular Biology 22 829 846 10.1007/BF00027369 10.1007/BF00027369 1:CAS:528:DyaK3sXms1CisLc%3D
33. S Marillonnet SR Wessler 1998 Extreme structural heterogeneity among the members of a maize Genetics 150 1245 1246 1:CAS:528:DyaK1cXnsFCntbs%3D
34. CL McIntyre BC Clarke R Appels 1988 Amplification and dispersion of repeated DNA sequences in the Triticeae Plant Systematics and Evolution 160 39 59 10.1007/BF00936708 10.1007/BF00936708 1:CAS:528:DyaL1cXls1Clur0%3D
35. CL McIntyre S Pereira LB Moran R Appels 1990 New Secale careale (rye) DNA derivatives for the detection of rye chromosome segments in wheat Genome 33 635 640 1:CAS:528:DyaK3MXktVaisrw%3D
36. ED Nagy T Lelley 2003 Genetic and physical mapping of sequence-specific amplified polymorphic (SSAP) markers on the 1RS chromosome arm or rye in a wheat background Theoretical and Applied Genetics 107 1271 1277 10.1007/s00122-003- 1367-0 10.1007/s00122-003-1367-0 1:CAS:528:DC%2BD3sXos1Okur4%3D (Pubitemid 37425006)
37. SR Pearce G Harrison JS Heslop-Harrison AJ Flavell A Kumar 1997 Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale careale) Genome 40 617 625 10.1139/g97-081 10.1139/g97-081 1:CAS:528:DyaK2sXntlSgtrg%3D
38. PM Rogowsky JY Liu S Manning C Taylor P Langridge 1992 Structural heterogeneity in the R173 family of rye-specific repetitive DNA sequences Plant Molecular Biology 20 95 102 10.1007/BF00029152 10.1007/BF00029152 1:CAS:528:DyaK38XmsVKgtbs%3D
39. PM Rogowsky S Manning JY Liu P Langridge 1991 The R173 family of rye-specific repetitive DNA sequences: A structural analysis Genome 34 88 95
40. P SanMiguel BS Gaut A Tikhonov Y Nakajima JL Bennetzen 1998 The paleontology of intergene retrotransposons of maize Nature Genetics 20 43 45 10.1038/1695 10.1038/1695 1:CAS:528:DyaK1cXmtVOmtL4%3D (Pubitemid 28410341)
41. DB Smith RB Flavell 1977 Nucleotide sequence organization in the rye genome Biochimica et Biophysica Acta 474 82 97 1:CAS:528:DyaE2sXltFOgtA%3D%3D
42. A Suoniemi K Anamthawat-Jonsson T Arna AH Schulman 1996 Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L) genome Plant Molecular Biology 30 1321 1329 10.1007/BF00019563 10.1007/BF00019563 1:CAS:528:DyaK28Xks1KisLc%3D
43. M Tomita K Shinohara M Morimoto 2008 Revolver is a new class of transposon-like gene composing the Triticeae genome DNA Research 15 49 62 10.1093/dnares/dsm029 10.1093/dnares/dsm029 1:CAS:528:DC%2BD1cXjvFemsbk%3D
44. AV Vershinin OG Alkhimova JS Heslop-Harrison 1996 Molecular diversification of tandemly organized DNA sequences and heterochromatic chromosome regions in some Triticeae species Chromosome Research 4 517 525 10.1007/BF02261779 10.1007/BF02261779 1:CAS:528:DyaK28XntlSktr0%3D
45. AV Vershinin T Schwarzacher JS Heslop-Harrison 1995 The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes The Plant Cell 7 1823 1833 10.2307/3870190 1:CAS:528: DyaK2MXpslOns7k%3D
46. JF Wendel 2000 Genome evolution in ployploids Plant Molecular Biology 42 225 249 10.1023/A:1006392424384 10.1023/A:1006392424384 1:CAS:528: DC%2BD3cXht1Grsrk%3D (Pubitemid 30096119)
47. FJ Zeller G Fischbec 1971 Cytologische Untersuchungen zur Identifizierung des Fremdchromosoms in derWeizensorte Zorba (W565) Z Pflanzenzuchtg 66 260 265