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. 1996 Aug 1;24(15):3017–3022. doi: 10.1093/nar/24.15.3017

Identification and distribution of seven classes of middle-repetitive DNA in the Arabidopsis thaliana genome.

H L Thompson 1, R Schmidt 1, C Dean 1
PMCID: PMC146053  PMID: 8760888

Abstract

In order to analyse further the genomic distribution of repetitive sequences in the Arabidopsis genome, we have identified and characterized seven novel repetitive sequences. Analysis of genomic representation, genomic location and DNA sequence divided the seven repeated sequences into two classes. The first was represented by three cosmid subclones (182A, 74A, 191A) carrying sequences that hybridised to up to 20 genomic fragments and showed sequence homology to the genes, Arabidopsis CCR2, Arabidopsis MYB and to various ATP-binding transport proteins. These multigene families mapped to various positions within the genome, as judged by hybridization to YAC clones constituting the Arabidopsis physical map. The second class was represented by four cosmid subclones (106B, 164A, 163A, 278A) that hybridised to between 20 and 300 genomic fragments. One of these, 106B, is a diverged, partial copy of the LTR of the Arabidopsis retrotransposon Athila. The other three sequences showed no homology to known genes or proteins. The distribution of these sequences on chromosome 4 was analysed and sequences hybridizing to 106B, 164A and 163A were found exclusively at the centromeric region of this chromosome. Their detailed arrangement at the centromeric region of chromosome 4, relative to other repeated sequence families and single copy sequences, was determined.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Avramova Z., SanMiguel P., Georgieva E., Bennetzen J. L. Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1. Plant Cell. 1995 Oct;7(10):1667–1680. doi: 10.1105/tpc.7.10.1667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baum M., Ngan V. K., Clarke L. The centromeric K-type repeat and the central core are together sufficient to establish a functional Schizosaccharomyces pombe centromere. Mol Biol Cell. 1994 Jul;5(7):747–761. doi: 10.1091/mbc.5.7.747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bauwens S., Van Oostveldt P., Engler G., Van Montagu M. Distribution of the rDNA and three classes of highly repetitive DNA in the chromatin of interphase nuclei of Arabidopsis thaliana. Chromosoma. 1991 Oct;101(1):41–48. doi: 10.1007/BF00360685. [DOI] [PubMed] [Google Scholar]
  4. Bedbrook J. R., Jones J., O'Dell M., Thompson R. D., Flavell R. B. A molecular description of telometic heterochromatin in secale species. Cell. 1980 Feb;19(2):545–560. doi: 10.1016/0092-8674(80)90529-2. [DOI] [PubMed] [Google Scholar]
  5. Bell C. J., Ecker J. R. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics. 1994 Jan 1;19(1):137–144. doi: 10.1006/geno.1994.1023. [DOI] [PubMed] [Google Scholar]
  6. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Carpenter C. D., Kreps J. A., Simon A. E. Genes encoding glycine-rich Arabidopsis thaliana proteins with RNA-binding motifs are influenced by cold treatment and an endogenous circadian rhythm. Plant Physiol. 1994 Mar;104(3):1015–1025. doi: 10.1104/pp.104.3.1015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Creusot F., Fouilloux E., Dron M., Lafleuriel J., Picard G., Billault A., Le Paslier D., Cohen D., Chabouté M. E., Durr A. The CIC library: a large insert YAC library for genome mapping in Arabidopsis thaliana. Plant J. 1995 Nov;8(5):763–770. doi: 10.1046/j.1365-313x.1995.08050763.x. [DOI] [PubMed] [Google Scholar]
  9. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hirochika H., Fukuchi A., Kikuchi F. Retrotransposon families in rice. Mol Gen Genet. 1992 May;233(1-2):209–216. doi: 10.1007/BF00587581. [DOI] [PubMed] [Google Scholar]
  11. Hirochika H., Hirochika R. Ty1-copia group retrotransposons as ubiquitous components of plant genomes. Jpn J Genet. 1993 Feb;68(1):35–46. doi: 10.1266/jjg.68.35. [DOI] [PubMed] [Google Scholar]
  12. Ish-Horowicz D., Burke J. F. Rapid and efficient cosmid cloning. Nucleic Acids Res. 1981 Jul 10;9(13):2989–2998. doi: 10.1093/nar/9.13.2989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. John B., Miklos G. L. Functional aspects of satellite DNA and heterochromatin. Int Rev Cytol. 1979;58:1–114. doi: 10.1016/s0074-7696(08)61473-4. [DOI] [PubMed] [Google Scholar]
  14. Konieczny A., Voytas D. F., Cummings M. P., Ausubel F. M. A superfamily of Arabidopsis thaliana retrotransposons. Genetics. 1991 Apr;127(4):801–809. doi: 10.1093/genetics/127.4.801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Moore G., Cheung W., Schwarzacher T., Flavell R. BIS 1, a major component of the cereal genome and a tool for studying genomic organization. Genomics. 1991 Jun;10(2):469–476. doi: 10.1016/0888-7543(91)90334-b. [DOI] [PubMed] [Google Scholar]
  16. Murphy T. D., Karpen G. H. Localization of centromere function in a Drosophila minichromosome. Cell. 1995 Aug 25;82(4):599–609. doi: 10.1016/0092-8674(95)90032-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Oppenheimer D. G., Herman P. L., Sivakumaran S., Esch J., Marks M. D. A myb gene required for leaf trichome differentiation in Arabidopsis is expressed in stipules. Cell. 1991 Nov 1;67(3):483–493. doi: 10.1016/0092-8674(91)90523-2. [DOI] [PubMed] [Google Scholar]
  18. Pruitt R. E., Meyerowitz E. M. Characterization of the genome of Arabidopsis thaliana. J Mol Biol. 1986 Jan 20;187(2):169–183. doi: 10.1016/0022-2836(86)90226-3. [DOI] [PubMed] [Google Scholar]
  19. Pélissier T., Tutois S., Deragon J. M., Tourmente S., Genestier S., Picard G. Athila, a new retroelement from Arabidopsis thaliana. Plant Mol Biol. 1995 Nov;29(3):441–452. doi: 10.1007/BF00020976. [DOI] [PubMed] [Google Scholar]
  20. Pélissier T., Tutois S., Tourmente S., Deragon J. M., Picard G. DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences. Genetica. 1996 Mar;97(2):141–151. doi: 10.1007/BF00054621. [DOI] [PubMed] [Google Scholar]
  21. Richards E. J., Ausubel F. M. Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell. 1988 Apr 8;53(1):127–136. doi: 10.1016/0092-8674(88)90494-1. [DOI] [PubMed] [Google Scholar]
  22. Richards E. J., Goodman H. M., Ausubel F. M. The centromere region of Arabidopsis thaliana chromosome 1 contains telomere-similar sequences. Nucleic Acids Res. 1991 Jun 25;19(12):3351–3357. doi: 10.1093/nar/19.12.3351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Schmidt R., West J., Love K., Lenehan Z., Lister C., Thompson H., Bouchez D., Dean C. Physical map and organization of Arabidopsis thaliana chromosome 4. Science. 1995 Oct 20;270(5235):480–483. doi: 10.1126/science.270.5235.480. [DOI] [PubMed] [Google Scholar]
  24. Simoens C. R., Gielen J., Van Montagu M., Inzé D. Characterization of highly repetitive sequences of Arabidopsis thaliana. Nucleic Acids Res. 1988 Jul 25;16(14B):6753–6766. doi: 10.1093/nar/16.14.6753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Snustad D. P., Haas N. A., Kopczak S. D., Silflow C. D. The small genome of Arabidopsis contains at least nine expressed beta-tubulin genes. Plant Cell. 1992 May;4(5):549–556. doi: 10.1105/tpc.4.5.549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Springer P. S., Edwards K. J., Bennetzen J. L. DNA class organization on maize Adh1 yeast artificial chromosomes. Proc Natl Acad Sci U S A. 1994 Feb 1;91(3):863–867. doi: 10.1073/pnas.91.3.863. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Staskawicz B., Dahlbeck D., Keen N., Napoli C. Molecular characterization of cloned avirulence genes from race 0 and race 1 of Pseudomonas syringae pv. glycinea. J Bacteriol. 1987 Dec;169(12):5789–5794. doi: 10.1128/jb.169.12.5789-5794.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Voytas D. F., Konieczny A., Cummings M. P., Ausubel F. M. The structure, distribution and evolution of the Ta1 retrotransposable element family of Arabidopsis thaliana. Genetics. 1990 Nov;126(3):713–721. doi: 10.1093/genetics/126.3.713. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Zachgo E. A., Wang M. L., Dewdney J., Bouchez D., Camilleri C., Belmonte S., Huang L., Dolan M., Goodman H. M. A physical map of chromosome 2 of Arabidopsis thaliana. Genome Res. 1996 Jan;6(1):19–25. doi: 10.1101/gr.6.1.19. [DOI] [PubMed] [Google Scholar]

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