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A complete BAC-based physical map of the Arabidopsis thaliana genome

Abstract

Arabidopsis thaliana is a small flowering plant that serves as the major model system in plant molecular genetics1. The efforts of many scientists have produced genetic maps that provide extensive coverage of the genome (http://genome-www.stanford.edu/Arabidopsis/maps.html). Recently, detailed YAC, BAC, P1 and cosmid-based physical maps (that is, representations of genomic regions as sets of overlapping clones of corresponding libraries) have been established that extend over wide genomic areas ranging from several hundreds of kilobases2,3 to entire chromosomes4,5,6,7,8,9. These maps provide an entry to gain deeper insight into the A. thaliana genome structure. A. thaliana has been chosen as the subject of the first large-scale project intended to determine the full genome sequence of a plant10. This sequencing project, together with the increasing interest in map-based gene cloning, has highlighted the requirement for a complete and accurate physical map of this plant species. To supply the scientific community with a high-quality resource, we present here a complete physical map of A. thaliana using essentially the IGF BAC library11. The map consists of 27 contigs that cover the entire genome, except for the presumptive centromeric regions, nucleolar organization regions (NOR) and telomeric areas. This is the first reported map of a complex organism based entirely on BAC clones and it represents the most homogeneous and complete physical map established to date for any plant genome. Furthermore, the analysis performed here serves as a model for an efficient physical mapping procedure using BAC clones that can be applied to other complex genomes.

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Figure 2: BAC-based physical map of the A. thaliana genome.

References

  1. 1

    Meinke, D.W., Cherry, J.M., Dean, C., Rounsley, S.D. & Koornneef, M. Arabidopsis thaliana: a model plant for genome analysis. Science 282, 662– 682 (1998).

    CAS  Article  Google Scholar 

  2. 2

    Bent, E., Johnson, S. & Bancroft, I. BAC representation of two low-copy regions of the genome of Arabidopsis thaliana. Plant J. 13, 849–855 (1998).

    CAS  Article  Google Scholar 

  3. 3

    Wang, M.L. et al. Construction of an ~2Mb contig in the region around 80 cM of Arabidopsis thaliana chromosome 2. Plant J. 12, 711–730 (1997).

    CAS  Article  Google Scholar 

  4. 4

    Schmidt, R. et al. Physical map and organisation of Arabidopsis thaliana chromosome 4. Science 270, 480– 483 (1995).

    CAS  Article  Google Scholar 

  5. 5

    Schmidt, R., Love, K., West, J., Lenehan, Z. & Dean, C. Description of 31 YAC contigs spanning the majority of Arabidopsis thaliana chromosome 5. Plant J. 11, 563–572 (1997).

    CAS  Article  Google Scholar 

  6. 6

    Kotani, H. et al. A fine physical map of Arabidopsis thaliana chromosome 5: construction of a sequence-ready contig map. DNA Res. 4, 371–378 (1997).

    CAS  Article  Google Scholar 

  7. 7

    Zachgo, E.A. et al. A physical map of chromosome 2 of Arabidopsis thaliana . Genome Res. 6, 19– 25 (1996).

    CAS  Article  Google Scholar 

  8. 8

    Camilleri, C. et al. A YAC contig map of Arabidopsis thaliana chromosome 3. Plant J. 14, 633–642 (1998).

    CAS  Article  Google Scholar 

  9. 9

    Sato, S. et al. A physical map of Arabidopsis thaliana chromosome 3 represented by two contigs of CIC YAC, P1, TAC and BAC clones. DNA Res. 5, 163–168 (1998).

    CAS  Article  Google Scholar 

  10. 10

    Bevan, M. et al. Objective: the complete sequence of a plant genome. Plant Cell 9, 476–478 ( 1997).

    CAS  Article  Google Scholar 

  11. 11

    Mozo, T., Fischer, S., Shizuya, H. & Altmann, T. Construction and characterisation of the IGF Arabidopsis BAC library. Mol. Gen. Genet. 258, 562–570 (1998).

    CAS  Article  Google Scholar 

  12. 12

    Mozo, T., Fischer, S., Meier-Ewert, S., Lehrach, H. & Altmann, T. Use of the IGF BAC library for physical mapping of the Arabidopsis thaliana genome. Plant J. 16, 377–384 (1998).

    CAS  Article  Google Scholar 

  13. 13

    Hoheisel, J.D. et al. High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe. Cell 73, 109–120 (1993).

    CAS  Article  Google Scholar 

  14. 14

    Palazzolo, M.J., Sawyer, S.A., Martin, C.H., Smoller, D.A. & Hartl, D.L. Optimised strategies for sequence-tagged-site selection in genome mapping. Proc. Natl Acad. Sci. USA 88, 8034–8038 (1991).

    CAS  Article  Google Scholar 

  15. 15

    Choi, S., Creelman, R.A., Mullet, J.E. & Wing, R. Construction and characterisation of a bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol. Biol. Rep. 13, 124–128 (1995).

    Article  Google Scholar 

  16. 16

    Marra, M. et al. A map for sequence analysis of the Arabidopsis thaliana genome. Nature Genet. 22, 265– 270 (1999).

    CAS  Article  Google Scholar 

  17. 17

    Lister, C. & Dean C. Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant J. 4, 745–750 ( 1993).

    CAS  Article  Google Scholar 

  18. 18

    Round, E.K., Flowers, S.K. & Richards, E.J. Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure. Genome Res. 7, 1045–1053 (1997).

    CAS  Article  Google Scholar 

  19. 19

    Copenhaver, G.P., Browne, W.E. & Preuss, D. Assaying genome-wide recombination and centromere functions with Arabidopsis tetrads. Proc. Natl Acad. Sci. USA 95, 247–252 (1998).

    CAS  Article  Google Scholar 

  20. 20

    Murata, M., Heslop-Harrison, J.S. & Motoyoshi, F. Physical mapping of the 5S ribosomal RNA genes in Arabidopsis thaliana by multi-colour fluorescence in situ hybridisation with cosmid clones. Plant J. 12, 31–37 (1997).

    CAS  Article  Google Scholar 

  21. 21

    Fransz, P. et al. Cytogenetics for the model system Arabidopsis thaliana. Plant J. 13, 867–876 (1998).

    CAS  Article  Google Scholar 

  22. 22

    Copenhaver, G.P. & Pikaard, C.S. Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenisation during concerted evolution. Plant J. 9, 273–282 (1996).

    CAS  Article  Google Scholar 

  23. 23

    Creusot, F. et al. The CIC library: a large insert YAC library for genome mapping in Arabidopsis thaliana. Plant J. 8, 763–770 (1995).

    CAS  Article  Google Scholar 

  24. 24

    Liu, Y.G., Mitsukawa, N., Lister, C., Dean, C. & Whittier, R.F. Isolation and mapping of a new set of 129 RFLP markers in Arabidopsis thaliana using recombinant inbred lines. Plant J. 10, 733– 736 (1996).

    CAS  Article  Google Scholar 

  25. 25

    Marra, M.A. et al. High throughput fingerprint analysis of large-insert clones. Genome Res. 7, 1072–1084 (1997).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank colleagues who contributed information before publication and L. Willmitzer for support during this work. T.M. was supported through a fellowship by the Max-Planck-Society.

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Correspondence to Thomas Altmann.

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Mozo, T., Dewar, K., Dunn, P. et al. A complete BAC-based physical map of the Arabidopsis thaliana genome . Nat Genet 22, 271–275 (1999). https://doi.org/10.1038/10334

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