Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana

Abstract

The plant Arabidopsis thaliana (Arabidopsis) has become an important model species for the study of many aspects of plant biology1. The relatively small size of the nuclear genome and the availability of extensive physical maps of the five chromosomes2,3,4 provide a feasible basis for initiating sequencing of the five chromosomes. The YAC (yeast artificial chromosome)-based physical map of chromosome 4 was used to construct a sequence-ready map of cosmid and BAC (bacterial artificial chromosome) clones covering a 1.9-megabase (Mb) contiguous region5, and the sequence of this region is reported here. Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases (kb), and 54% of the predicted genes had significant similarity to known genes. Other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, the frequent occurrence of clustered gene families, and the sequence of several classes of genes not previously encountered in plants.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: This map shows the positions of genes, predicted genes and other features.
Figure 2: The pie chart shows the proportion of predicted genes with assigned cellular roles in each of the functional categories described in Table 2.

Similar content being viewed by others

References

  1. Meyerowitz, E. M. & Somerville, C. R. (eds) Arabidopsis (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1994).

    Google Scholar 

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

    Article  ADS  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  4. 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).

    Article  CAS  PubMed  Google Scholar 

  5. Bancroft, I.et al. Astrategy involving the use of high-redundancy YAC subclone libraries facilitates the contiguous representation in cosmid and BAC clones of 1.7 Mb of the genome of Arabidopsis thaliana. Weeds World 4, 1–9 (1997).

    CAS  Google Scholar 

  6. Sato, S.et al. Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones. DNA Res. 4, 215– 230 (1997).

    Article  CAS  PubMed  Google Scholar 

  7. Pearson, W. R. & Lipman, D. J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85, 2444–2448 (1988).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  8. Riley, M. Functions of gene products in E. coli. Microbiol. Rev. 57, 862–952 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Mewes, H.-W.et al. Overview of the yeast genome. Nature 387 (suppl.) 7–84 (1997).

    Google Scholar 

  10. White, S. E., Habera, L. F. & Wessler, S. R. Retrotransposons in the flanking regions of normal plant genes: A role for copia-like elements in the evolution fo gene structure and expression. Proc. Natl Acad. Sci. USA 91, 11792–11796 (1994).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  11. Konieczny, A., Voytas, D. F., Cummings, M. P. & Ausubel, F. M. Asuperfamily of Arabidopsis thaliana retrotransposons. Genetics 127, 801–809 ( 1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. SanMiguel, P.et al. Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765– 768 (1996).

    Article  ADS  CAS  PubMed  Google Scholar 

  13. Wessler, S. R., Bureau, T. E. & White, S. E. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5, 814–821 (1995).

    Article  CAS  PubMed  Google Scholar 

  14. Parker, J. E.et al. The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the Toll and interleukin-1 receptors with N and L6. The Plant Cell 9, 879 –894 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Pear, J. R., Kawagoe, Y., Screckengost, W. E., Delmer, D. P. & Stalker, D. M. Higher plants contain homologues of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. Proc. Natl Acad. Sci. USA 93, 12637–12642 (1996).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  16. Back, K. & Chappell, J. Cloning and bacterial expression of a sesquiterpene cyclase from Hyoscamus muticus and its molecular comparison to related terpene cyclases. J. Biol. Chem. 270, 7375–7381 (1995).

    Article  CAS  PubMed  Google Scholar 

  17. Gavin, K. A., Hidaka, M. & Stillman, B. Conserved initiator proteins in eukaryotes. Science 270, 1667–1671 ( 1995).

    Article  ADS  CAS  PubMed  Google Scholar 

  18. Fishel, R.et al. The human mutator gene homologue MHS2 and its association with hereditary nonpolyposis colon cancer. Cell 75, 1027 –1038 (1993).

    Article  CAS  PubMed  Google Scholar 

  19. Marcus, G. A., Silverman, N., Berger, S. L., Horiuchi, J. & Guarente, L. Functional similarity and physical association between GCN5 and ADA2: putative transcriptional adaptors. EMBO J. 13, 4807–4815 ( 1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Neuwald, A. F. & Landsman, D. GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Trends Biochem. Sci. 22, 154–155 (1997).

    Article  CAS  PubMed  Google Scholar 

  21. Oppenheimer, D. G.et al. Essential role for a kinesin-like protein in Arabidopsis trichome morphogenesis. Proc. Natl Acad. Sci. USA 94, 6261–6266 (1997).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  22. Pongs, O.et al. Frequenin–a novel calcium-binding protein that modulates synaptic efficacy in the Drosophila nervous system. Neuron 11, 15–28 (1993).

    Article  CAS  PubMed  Google Scholar 

  23. Friesen, H., Lunz, R., Doyle, S. & Segall, J. Mutation in the SPS1-encoded protein kinase of Saccharomyces cerevisiae leads to defects in transcription and morphology during spore formation. Genes Dev. 8, 2162–2175 (1994).

    Article  CAS  PubMed  Google Scholar 

  24. Gabor Miklos, G. & Rubin, G. M. The role of the genome project in determining gene function: Insights from model organisms. Cell 86, 521–529 (1996).

    Article  Google Scholar 

  25. Wilson, R.et al. 2.2Mb of contiguous nucleotide sequence from chromosome III of C. elegans . Nature 368, 32–38 (1994).

    Article  ADS  CAS  PubMed  Google Scholar 

  26. Meyerowitz, E. M. Plants and the logic of development. Genetics 145, 5–9 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Bent, E., Johnson, S., Bancroft, I. BAC representation of two low-copy regions of the genome of Arabidopsis thaliana. The Plant J. (in the press).

  28. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article  CAS  PubMed  Google Scholar 

  29. Hebsgaard, S. M.et al. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res. 24, 3439–3452 ( 1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was initiated and sponsored by the European Commission, DG-XII Life Sciences. Additional support from the BBSRC Plant and Animal Genome Analysis Programme, GREG (Groupe de Recherche et d'Etude des Genomes), BioResearch Ireland, and Plan Nacional de Investigacion Cientifica y Technica is gratefully acknowledged.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to M. Bevan.

Rights and permissions

Reprints and permissions

About this article

Cite this article

The EU Arabidopsis Genome Project, Bevan, M., Bancroft, I. et al. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391, 485–488 (1998). https://doi.org/10.1038/35140

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/35140

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing