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A map for sequence analysis of the Arabidopsis thaliana genome

Nature Genetics volume 22, pages 265–270 (1999)Cite this article

Abstract

Arabidopsis thaliana has emerged as a model system for studies of plant genetics and development, and its genome has been targeted for sequencing1 by an international consortium (the Arabidopsis Genome Initiative; http://genome-www.stanford.edu/Arabidopsis/agi.html). To support the genome-sequencing effort, we fingerprinted more than 20,000 BACs (ref. 2) from two high-quality publicly available libraries3,4,5, generating an estimated 17-fold redundant coverage of the genome, and used the fingerprints to nucleate assembly of the data by computer. Subsequent manual revision of the assemblies resulted in the incorporation of 19,661 fingerprinted BACs into 169 ordered sets of overlapping clones ('contigs'), each containing at least 3 clones. These contigs are ideal for parallel selection of BACs for large-scale sequencing and have supported the generation of more than 5.8 Mb of finished genome sequence submitted to GenBank; analysis of the sequence has confirmed the integrity of contigs constructed using this fingerprint data. Placement of contigs onto chromosomes can now be performed, and is being pursued by groups involved in both sequencing and positional cloning studies. To our knowledge, these data provide the first example of whole-genome random BAC fingerprint analysis of a eucaryote, and have provided a model essential to efforts aimed at generating similar databases of fingerprint contigs to support sequencing of other complex genomes, including that of human.

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Figure 1: A. thaliana BAC DNAs, digested with HindIII and visualized on a SYBR green-stained 1% agarose fingerprinting gel6.
Figure 2: Editing auto-assemblies tends to increase the number of clones per contig.
Figure 3: Display of the contig, fingerprint and size data in FPC ( ref.17)
Figure 4: Comparison of fingerprint- and sequence-based restriction fragment sizes.

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Acknowledgements

We thank T. Altmann and R. Wing for providing the scientific community access to their high-quality A. thaliana BAC libraries; E. Mardis, S. Chissoe, W. Barbazuk and S. Gorski for comments and discussion; D. Panussis for design and engineering expertise; M. Holman for maintaining data in web-accessible formats; C. McCabe, N. Florence, D. Scheer, S. Sasso, L. Belaygorod and C. Franklin for expert assistance in fingerprinting; A. Favello for laboratory management; staff at Washington University Genome Sequencing Center for technical support; and D. Preuss, G. Copenhaver, T. Kuromori and many others for providing contig anchoring information. Funding for this work was provided by Monsanto Company.

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Authors and Affiliations

  1. Washington University Genome Sequencing Center, 4444 Forest Park Boulevard, St Louis, 63108, Missouri, USA

    Marco Marra, Tamara Kucaba, Mandeep Sekhon, LaDeana Hillier, Asif Chinwalla, Jye'mon Crockett, Jacqueline Fedele, Heather Grover, Christopher Gund, Ken McDonald, John McPherson, Nancy Mudd, Jacqueline Schein, Ryan Seim, Proteon Shelby, Robert Waterston & Richard Wilson

  2. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, 11724 , New York, USA

    Robert Martienssen, W. Richard McCombie & Larry Parnell

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Correspondence to Marco Marra.

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Marra, M., Kucaba, T., Sekhon, M. et al. A map for sequence analysis of the Arabidopsis thaliana genome . Nat Genet 22, 265–270 (1999). https://doi.org/10.1038/10327

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