Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Isolation and identification of a non-specific tandemly repeated DNA sequence in Oryza species


A tandemly repeated DNA sequence (RRS7) was isolated from Oryza alta (CCDD). RRS7-related sequences were also found tandemly arrayed in genomes AA, BB, BBCC, CC, and EE, and a small amount of RRS7-related sequences were detected in genome FF and the Oryza species with unknown genomes. DNA sequence analysis of the 1844-bp insert of RRS7 revealed that it contained six tandemly repeated units, of which five were 155 bp in length and one was 194 bp in length and contained an imperfect internal 39-bp duplication. Southern blot analysis showed that the boundary sequence contained in RRS7 is a single-copy sequence. A 155-bp consensus sequence derived from the six monomeric repeats contained no internal repeat and showed no significant homology to other currently known sequences. The results of Southern blot and sequence analysis revealed that there are at least two subfamilies present in the RRS7 family; these are represented by the DraI site and the MspI site, respectively. Restriction digestion with two pairs of isoschizomers MboI/Sau3A and MspI/HpaII demonstrated that most of the C residues in the GATC sites and the internal C in the CCGG sites of the RRS7 family in O. Alta were methylated. The usefulness of the RRS7 family in determining the evolutionary relationship of the genome DD and other Oryza genomes is discussed.

This is a preview of subscription content, log in to check access.


  1. Arumanagathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:229–241

  2. Aswidinnoor H, Nelson RJ, Dallas JF, Mcintyre CL, Leung H, Gustafson JP (1991) Cloning and characterization of repetitive DNA sequences from genomes of Oryza minuta and Oryza australiensis. Genome 34:790–798

  3. Brutlug DL (1980) Molecular arrangement and evolution of heterochromatic DNA. Annu Rev Genet 14:121–144

  4. Deshpande VG, Ranjekar PK (1980) Repetitive DNA in three Gramineae species with low DNA content. Hoppe-seyleris Z Physiol Chem 361:S 1223–1233

  5. Dover G (1982) Molecular drive: a cohesive mode of species evolution. Nature 299:111–117

  6. Dover G (1986) Molecular drive in multigene families: how biological novelties arise, spread and are assimilated. Trends Genet 168: 159–165

  7. Evans IJ, James AM, Barnes SR (1983) Organization and evolution of repeated DNA sequences in closely related plant genomes. J Mol Biol 170:803–826

  8. Flavell R (1980) The molecular characterization and organization of plant chromosome DNA sequences. Annu Rev Plant Physiol 31: 569–596

  9. Hemleben V, Zentgraf U, King K, Borisjuk N, Schweizer G (1992) Middle repetitive and highly repetitive sequences detect polymorphisms in plants. In: Kahl G, Appelhans H, Kompf J, Driesel AJ (eds) DNA polymorphisms in eucaryotic genomes. Huthig, Heidelberg, pp 157–170

  10. Ingham LD, Hanna WW, Baier JW, Hannah LC (1993) Origin of the main class of repetitive DNA with selected Pennisetum species. Mol Gen Genet 238:350–356

  11. Jena KK, Khush GS (1989) Cytogenetic relationships among the three species of Oryza latifolia complex. Rice Genet Lett 5:74–75

  12. McCouch SR, Kocket G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829

  13. Miklos GLG (1985) Localized highly repetitive DNA in vertebrate and invertebrate genomes. In: MacIntype (ed) Molecular evolutionary genetics. Plenum Press, New York, pp 241–319

  14. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

  15. Singer MF (1982) Highly repeated sequences in mamalian genomes. Int Rev Cytol 76:67–112

  16. Southern EM (1975) Long range periodicities in mouse satellite DNA. J Mol Biol 94:51–69

  17. Vaughan DA (1994) The wild relatives of rice: a genetic resources handbook. International Rice Research Institute, Los Banos, Philippines

  18. Waye JS, Willard HF (1987) Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes. Nucleic Acids Res 15: 7549–7569

  19. Wu T, Wu R (1992) A novel repetitive DNA sequence in the genus Oryza. Theor Appl Genet 84:136–144

  20. Xin ZY, Appels R (1988) Occurrence of rye (Secale cereale) 350-bp family DNA sequences in Agropyron and other Triticeae. Plant Syst Evol 160:65–76

  21. Zhao X, Wu T, Xie Y, Wu R (1989) Genome-specific repetitive sequences in the genus Oryza. Theor Appl Genet 78:201–209

Download references

Author information

Additional information

Communicated by M. Koornneef

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Li, X.B., Liang, C.Z., Wu, H.G. et al. Isolation and identification of a non-specific tandemly repeated DNA sequence in Oryza species. Theoret. Appl. Genetics 92, 702–708 (1996).

Download citation

Key words

  • Oryza
  • Tandemly repeated DNA sequence
  • Restriction fragment length polymorphism (RFLP)