Chromosoma

, Volume 113, Issue 6, pp 276–283 | Cite as

Satellite repeats in the functional centromere and pericentromeric heterochromatin of Medicago truncatula

  • Olga Kulikova
  • René Geurts
  • Monique Lamine
  • Dong-Jin Kim
  • Douglas R. Cook
  • Jack Leunissen
  • Hans de Jong
  • Bruce A. Roe
  • Ton Bisseling
Research Article

Abstract

Most eukaryotic centromeres contain long arrays of tandem repeats, with unit lengths of 150–300 bp. We searched for such repeats in the functional centromeres of the model legume Medicago truncatula (Medicago) accession Jemalong A17. To this end three repeats, MtR1, MtR2 and MtR3, were identified in 20 Mb of a low-pass, whole genome sequencing data set generated by a random shotgun approach. The nucleotide sequence composition, genomic organization and abundance of these repeats were characterized. Fluorescent in situ hybridization of these repeats on chromosomes at meiosis I showed that only the MtR3 repeat, encompassing stretches of 450 kb to more than 1.0 Mb, is located in the functional portion of all eight centromeres. MtR1 and MtR2 occupy distinct regions in pericentromeric heterochromatin. We also studied the presence and distribution of MtRs in Medicago accession R108-1, a genotype with a genome that is 20% smaller than that of Jemalong A17. We determined that while MtR3 is also centromeric on all pachytene bivalents in R108-1, MtR1 and MtR2 are not present in the R108 genome.

References

  1. Agarwal K, Gupta PK (1983) Cytological studies in the genus Medicago Linn. Cytologia 48:781–793Google Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Nucleic Acids Res 25:3389–3402PubMedGoogle Scholar
  4. Blondon F, Marie D, Brown S, Kondorosi A (1994) Genome size and base composition in Medicago sativa and M. truncatula species. Genome 37:264–275Google Scholar
  5. Bodenteich A, Chissoe S, Wang YF, Roe BA (1993) Shotgun cloning as the strategy of choice to generate templates for high-throughput dideoxynucleotide sequencing. In: Venter JC (ed) Automated DNA sequencing and analysis techniques. Academic, London, pp 42–50Google Scholar
  6. Campell BR, Soung Y, Posch TE, Cullis CA, Town CD (1992). Sequence and organization of 5S ribosomal RNA-encoding genes of Arabidopsis thaliana. Gene 112:225–228CrossRefPubMedGoogle Scholar
  7. Cheng Z, Donga F, Langdon T, Ouyang S, Buell CR, Gu M, Blattner FR, Jiang J (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691–1704CrossRefPubMedGoogle Scholar
  8. Chissoe SL, Bodenteich A, Wang YF, Wang YP, Burian D, Clifton SW, Crabtree J, Freeman A, Iyer K, Jian L, Ma Y, McLaury HJ, Pan HQ, Sharon O, Toth S, Wong Z, Zhang G, Heisterkamp N, Groffen J, Roe BA (1995) Sequence and analysis of the human ABL gene, BCR gene and regions involved in the Philadelphia chromosomal translocation. Genomics 27:67–82CrossRefPubMedGoogle Scholar
  9. Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis THN, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA (in press)Google Scholar
  10. Csink AK, Henikoff S (1998) Something from nothing: the evolution and utility of satellite repeats. Trends Genet 14:200–204Google Scholar
  11. Ewing B, Green P (1998) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194PubMedGoogle Scholar
  12. Ewing B, Hillier L, Wendl M, Green P (1998) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185PubMedGoogle Scholar
  13. Galasso I, Schmidt T, Pignone D, Heslop-Harrison JS (1995) The molecular cytogenetics of Vigna unguiculata (L.) Walp: the physical organization and characterization of 18S–5.8S–25S rRNA genes, 5S rRNA genes, telomere-like sequences, and a family of centromeric repetitive DNA sequences. Theor Appl Genet 928:935Google Scholar
  14. Gerbach M, Kevel Z, Siljak-Yakovlev S, Kondorosi E, Kondorosi A, Trinh TH (1999) FISH chromosome mapping allowing karyotype analysis in Medicago truncatula Jemalong J5 and R-108-1. Mol Plant Microbe Interact 12:947–950Google Scholar
  15. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202PubMedGoogle Scholar
  16. Hall SE, Kettler G, Preuss D (2003) Centromere satellites from Arabidopsis populations: maintenance of conserved and variable domains. Genome Res 13:195–205CrossRefPubMedGoogle Scholar
  17. Hall AE, Keith KC, Hall SE, Copenhaver GP, Preuss D (2004) The rapidly evolving field of plant centromeres. Curr Opin Plant Biol 7:108–114CrossRefPubMedGoogle Scholar
  18. Henikoff S, Ahmad K, Malik HS (2001) The centromere complex: Stable inheritance with rapidly evolving DNA. Science 293:1098–1102CrossRefPubMedGoogle Scholar
  19. Heslop-Harrison JS (2000) Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 12:617–635CrossRefPubMedGoogle Scholar
  20. Heslop-Harrison JS, Brandes A, Schwarzacher T (2003) Tandemly repeated DNA sequences and centromeric chromosomal region of Arabidopsis species. Chromosome Res 11:241–253CrossRefPubMedGoogle Scholar
  21. Hoffmann B, Trinh TH, Leung J, Kondorosi A, Kondorosi E (1997) A new Medicago truncatula line with superior in vitro regeneration, transformation, and symbiotic properties isolated through cell culture selection. Mol Plant Microbe Interact 10:307–315Google Scholar
  22. Houben A, Schubert I (2003) DNA and proteins of plant centromeres. Curr Opin Plant Biol 6:554–560CrossRefPubMedGoogle Scholar
  23. Jiang J, Birchler J, Parrott W, Dawe R (2003) A molecular view of plant centromeres. Trends Plant Sci 8:570–575CrossRefPubMedGoogle Scholar
  24. Kaszas E, Birchler JA (1998) Meiotic transmission rates correlate with physical features of rearranged centromeres in maize. Genetics 150:1683–1692PubMedGoogle Scholar
  25. Kulikova O, Gualtieri G, Geurts R, Kim D-J, Cook D, Huguet T, de Jong H, Fransz P, Bisseling T (2001) Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J 27:49–58CrossRefPubMedGoogle Scholar
  26. Lamb JC, Theuri J, Birchler JA (2004) What’s in a centromere? Genome Biol 5:239CrossRefPubMedGoogle Scholar
  27. Maluszynska J, Heslop-Harrison JS (1991) Localization of tandemly repeated DNA sequences in Arabidopsis thaliana. Plant J 1:159–166CrossRefGoogle Scholar
  28. Martinez-Zapater JM, Estelle MA, Somerville CR (1986) A highly repeated DNA sequence in Arabidopsis thaliana. Mol Gen Genet 204:417–423Google Scholar
  29. Morgante M, Jurman I, Zhu T, Keim P, Rafalski JA (1997) The STR120 satellite DNA of soybean: organization, evolution and chromosomal specificity. Chromosome Res 5:363–373CrossRefPubMedGoogle Scholar
  30. Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36:138–145CrossRefPubMedGoogle Scholar
  31. Ohmido N, Kijima K, Akiyama Y, de Jong JH, Fukui K (2000) Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice. Mol Gen Genet 263:388–394CrossRefPubMedGoogle Scholar
  32. Pan HQ, Wang YP, Chissoe SL, Bodenteich A, Wang Z, Iyer K, Clifton SW, Crabtree JS, Roe BA (1994) The complete nucleotide sequence of the SacBII domain of the P1 pAD10-SacBII cloning vector and three cosmid cloning vectors: pTCF, svPHEP and LAWRIST16. GATA 11:181–186Google Scholar
  33. Parsons JD (1995) Miropeats: graphical DNA sequence comparisons. Comput Appl Biosci 11:615–619PubMedGoogle Scholar
  34. Rogers SO, Bendish AJ (1988) Extraction of DNA from plant tissue. In: Gelvin SB, Schilperoort RA (eds) Plant molecular manual. Kluwer, Dordrecht, pp 1–10Google Scholar
  35. Ross K, Fransz PF, Jones GH (1996) A light microscopic atlas of meiosis in Arabidopsis thaliana. Chromosome Res 4:507–516PubMedGoogle Scholar
  36. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, vols 1–3. Cold Spring Harbor Laboratory, NYGoogle Scholar
  37. Sun X, Wahlstrom J, Karpen GH (1997) Molecular structure of a functional Drosophila centromere. Cell 92:1007–1019CrossRefGoogle Scholar
  38. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedGoogle Scholar
  39. Wevrick R, Willard HF (1989) Long-range organization of tandem arrays of a satellite DNA at the centromeres of human chromosomes: high frequency array-length polymorphism and meiotic stability. Proc Natl Acad Sci USA 86:9394–9398PubMedGoogle Scholar
  40. Wu J, Yamagata H, Hayashi-Tsugane M, Hijishita S, Fujisawa M, Shibata M, Ito Y, Nakamura M, Sakaguchi M, Yoshihara R, Kobayashi H, Ito K, Karasawa W, Yamamoto M, Saji S, Katagiri S, Kanamori H, Namiki N, Katayose Y, Matsumoto T, Sasaki T (2004) Composition and structure of the centromeric region of rice chromosome 8. Plant Cell 16:967–976CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Olga Kulikova
    • 1
  • René Geurts
    • 1
  • Monique Lamine
    • 1
  • Dong-Jin Kim
    • 2
  • Douglas R. Cook
    • 2
  • Jack Leunissen
    • 3
  • Hans de Jong
    • 4
  • Bruce A. Roe
    • 5
  • Ton Bisseling
    • 1
  1. 1.Laboratory of Molecular Biology, Department of Plant SciencesWageningen UniversityWageningenThe Netherlands
  2. 2.Department of Plant PathologyUniversity of CaliforniaDavisUSA
  3. 3.Laboratory of Bioinformatics, Department of Plant SciencesWageningen UniversityWageningenThe Netherlands
  4. 4.Laboratory of Genetics, Department of Plant SciencesWageningen UniversityWageningenThe Netherlands
  5. 5.Department of Chemistry and BiochemistryThe University of OklahomaNormanUSA

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