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Genomic sequence sampling: a strategy for high resolution sequence–based physical mapping of complex genomes

Nature Genetics volume 7, pages 40–47 (1994)Cite this article

Abstract

We present a simple and efficient method for constructing high resolution physical maps of large regions of genomic DNA based upon sampled sequencing. The physical map is constructed by ordering high density cosmid contigs and determining a sequence fragment from each end of every clone. The resulting map, which contains 30–50% of the complete DNA sequence, allows the identification of many genes and makes possible PCR amplification of virtually any part of the genome. We apply this strategy to the automated analysis of the genome of the primitive eukaryote Giardia lamblia and evaluate its applicability to the physical mapping and DNA sequencing of the human genome.

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References

  1. Schwartz, D. & Cantor, C. Separation of yeast chromosome-sized DNAs by pulsed field gradient electrophoresis. Cell 37, 67–75 (1984).

    Article  CAS  Google Scholar 

  2. Cox, D.R. et al. Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science 250, 245–250 (1990).

    Article  CAS  Google Scholar 

  3. Bellanne-Chantelot, C. et al. Mapping the whole human genome by fingerprinting yeast artificial chromosomes. Cell 70, 1059–1068 (1992).

    Article  CAS  Google Scholar 

  4. Poustka, A.M. & Lehrach, H. Jumping libraries and linking libraries; The next generation tools in mammalian genetics. Trends Genetics 2, 174–179 (1986).

    Article  CAS  Google Scholar 

  5. Coulson, A. et al. Toward a physical map of the genome of the nemotode Ceanorhabditus elegans. Proc. natn. Acad. Sci. U.S.A. 83, 7821–7825 (1986).

    Article  CAS  Google Scholar 

  6. 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).

    Article  CAS  Google Scholar 

  7. Mott, R. et al. Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe. Nucl. Acids Res. 21, 1965–1974 (1993).

    Article  CAS  Google Scholar 

  8. Kohara, Y. et al. The physical map of the whole E. coil chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50, 495–508 (1987).

    Article  CAS  Google Scholar 

  9. Olson, M.V. et al. Random-clone strategy for genomic restriction mapping in yeast. Proc. natn. Acad. Sci. U.S.A. 83, 7826–7830 (1986).

    Article  CAS  Google Scholar 

  10. Riles, L. et al. Physical maps of the six smallest chromosomes of Saccharomyces cerevisiae at a resolution of 2.6 kilobase pairs. Genetics 134, 81–150 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Mizukami, T. et al. A 13 kb resolution cosmid map of the 14 Mb fission yeast genome by nonrandom sequence-tagged site mapping. Cell 73, 121–32 (1993).

    Article  CAS  Google Scholar 

  12. Foote, S. et al. The human Y chromosome: overlapping DNA clones spanning the euchromatic region. Science 258, 60–66 (1992).

    Article  CAS  Google Scholar 

  13. Chumakov, I. et al. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature 359, 380–387 (1992).

    Article  CAS  Google Scholar 

  14. Burland, V. et al. DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16, 551–561 (1993).

    Article  CAS  Google Scholar 

  15. Daniels, D.L. et al. Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257, 771–778 (1992).

    Article  CAS  Google Scholar 

  16. Plunkett, G.3. et al. Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucl. Acids Res. 21, 3391–3398 (1993).

    Article  CAS  Google Scholar 

  17. Oliver, S.G. et al. The complete DNA sequence of yeast chromosome III. Nature 357, 38–46 (1992).

    Article  CAS  Google Scholar 

  18. Martin-Gallardo, A. et al. Automated DNA sequencing and analysis of 106 kilobases from human chromosome 19q13.3. Nature Genet. 1, 34–39 (1992).

    Article  CAS  Google Scholar 

  19. Wilson, R.K. et al. Nucleotide sequence analysis of 95 kb near the 3′ end of the murine T-cell receptor alpha/delta chain locus: strategy and methodology. Genomics 13, 1198–1208 (1992).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  21. Adams, M.D. et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651–1656 (1991).

    Article  CAS  Google Scholar 

  22. Adams, M.D. et al. Sequence identification of 2,375 human brain genes. Nature 355, 632–634 (1992).

    Article  CAS  Google Scholar 

  23. Adams, M.D. et al. 3,400 new expressed sequecne tags identify diversity of transcripts in human brain. Nature Genet. 4, 256–267 (1993).

    Article  CAS  Google Scholar 

  24. Polymeropoulos, M.H. et al. Chromosomal distribution of 320 genes from a brain cDNA library. Nature Genet. 4, 381–386

    Article  CAS  Google Scholar 

  25. Olson, M. et al. A common language for physical mapping of the human genome. Science 245, 1434–1435 (1989).

    Article  CAS  Google Scholar 

  26. Green, E.D. et al. Systematic generation of sequence-tagged sites for physical mapping of human chromosomes: application to the mapping of human chromosome 7 using yeast artificial chromosomes. Genomics 11, 548–564 (1991).

    Article  CAS  Google Scholar 

  27. Smith, M.W. et al. A sequence-tagged site map of human chromosome 11. Genomics 17, 699–725 (1993).

    Article  CAS  Google Scholar 

  28. Evans, G.A. & Lewis, K.A. Physical mapping of complex genomes by cosmid multiplex analysis. Proc. natn. Acad. Sci. U.S.A. 86, 5030–5034 (1989).

    Article  CAS  Google Scholar 

  29. Altschul, S.F. et al. Basic local alignment search tool. J. molec. Biol. 215, 403–410 (1990).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  31. Uberbacher, E.C. & Mural, R.J. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. natn. Acad. Sci. U.S.A. 88, 11261–11265 (1991).

    Article  CAS  Google Scholar 

  32. Weissenbach, J. et al. A second-generation linkage map of the human genome. Nature 359, 794–801 (1992).

    Article  CAS  Google Scholar 

  33. Kieleczawa, J. et al. DNA sequencing by primer walking with strings of contiguous hexamers. Science 258, 1787–1791 (1992).

    Article  CAS  Google Scholar 

  34. Strathmann, M. et al. Transposon-facilitated DNA sequencing. Proc. natn. Acad. Sci. U.S.A. 88, 1247–1250 (1991).

    Article  CAS  Google Scholar 

  35. Deaven, L.L. et al. Construction of human chromosome-specific DNA libraries from flow sorted chromosomes. Cold Spring Harbor Symp. Quant. Biol. 51, 159–167 (1986).

    Article  CAS  Google Scholar 

  36. Fan, J.B. et al. Giardia lamblia: haploid genome size determined by pulsed field gel electrophoresis is less than 12 Mb. Nucl. Acids Res. 19, 1905–1908 (1991).

    Article  CAS  Google Scholar 

  37. Adam, R.D. The biology of Giardia spp. Microbiol. Rev. 55, 706–732 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Sogin, M.L. et al. Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science 243, 75–77 (1989).

    Article  CAS  Google Scholar 

  39. Evans, G.A. et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 79, 9–20 (1989).

    Article  CAS  Google Scholar 

  40. Holberton, D. et al. Segmented alpha-helical coiled-coil structure of the protein giardin from the Giardia cytoskeleton. J. molec. Biol. 204, 789–795 (1988).

    Article  CAS  Google Scholar 

  41. Aggarwal, A. et al. A heat shock protein gene in Giardia lamblia unrelated to HSP70. Nucl. Acids Res. 18, 3409 (1990).

    Article  CAS  Google Scholar 

  42. Soderlund, C.A. et al. in Proceedings of the 26th Hawaii International Conference on System Sciences: Biotechnology Computing. (ed. Hunter, L.) 620–630 (CA: IEEE Computer Society Press, 1993).

    Google Scholar 

  43. Soderlund, C.A. & Burks, C. GRAM and genfragII: solving and testing the single-digest partially-ordered restriction map problem. Comp. Appl. Biol. Sci. (in the press).

  44. Saiki, R.K. et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491 (1988).

    Article  CAS  Google Scholar 

  45. Cohen, D. et al. A first-generation physical map of the human genome. Nature 366, 698–701 (1993).

    Article  CAS  Google Scholar 

  46. Coulson, A. et al. Genome linking with yeast artificial chromosomes. Nature 335, 184–186 (1988).

    Article  CAS  Google Scholar 

  47. Baxendale, S. et al. A cosmid contig and high resolution restriction map of the 2 megabase region containing the Huntington's disease gene. Nature Genet. 4, 181–6 (1993).

    Article  CAS  Google Scholar 

  48. Ansorge, W. et al. High-throughput automated DNA sequencing facility with fluorescent labels at the European Molecular Biology Laboratory. Electrophoresis 13, 616–619 (1992).

    Article  CAS  Google Scholar 

  49. Drmanac, R. et al. DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing. Science 260, 1649–1652 (1993).

    Article  CAS  Google Scholar 

  50. Drury, H.A. et al. A graphical user interface for quantitative Imaging and analysis of electrophoretic gels and autoradiograms. Biotechniques 12, 892–898 (1992).

    CAS  PubMed  Google Scholar 

  51. Sambrook, J. et al. Laboratory cloning: a laboratory manual. A.2.I (Cold Spring Harbor Press, New York, 1988).

    Google Scholar 

  52. Feinberg, A.P. & Vogelstein, B. Addenddum. A technique for radiolabeiing DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 137, 266–267 (1984).

    Article  CAS  Google Scholar 

  53. Church, G.M. & Gilbert, W. Genomic sequencing. Proc. natn. Acad. Sci. U.S.A. 81, 1991–1995 (1984).

    Article  CAS  Google Scholar 

  54. Doolittle, R.F. & Feng, D.-F. in Molecular evolution: computer analysis of protein and nucleic acid sequences, (ed. Doolittle, R.F.) 659–669 (Academic Press, New York, 1990).

    Google Scholar 

  55. Feng, D.-F. & Doolittle, R.F. in Molecular evolution: computer analysis of protein and nucleic acid sequences, (ed. Doolittle, R.F.) 375–387 (Academic Press, New York, 1990).

    Google Scholar 

  56. Clark, S.P. et al. in Biocomputing: Genome sequence analysis (ed. Smith, D. W.) 13–49 (Academic Press, New York).

  57. Stallings, R.L. et al. Evaluation of a cosmid contig physical map of human chromosome 16. Genomics 13, 1031–1039 (1992).

    Article  CAS  Google Scholar 

  58. Fonstein, M. et al. Physical map of the genome of Rhodobacter capsulatus SB 1003. J. Bacteriol. 174, 4070–4077 (1992).

    Article  CAS  Google Scholar 

  59. Tynan, K. et al. Assembly and analysis of cosmid contigs in the CEA-gene family region of human chromosome 19. Nucl. Acids Res. 20, 1629–1636 (1992).

    Article  CAS  Google Scholar 

  60. Lander, E.S. & Waterman, M.S. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2, 231–239 (1988).

    Article  CAS  Google Scholar 

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Author notes

  1. Michael W. Smith: Address after July 1994

Authors and Affiliations

  1. Molecular Genetics Laboratory, The Salk Institute for Biological Studies, La Jolla, California, 92037, USA

    Michael W. Smith, Anita L. Holmsen, Yalin H. Wei, Melinda Peterson & Glen A. Evans

  2. Biological Carcinogenesis and Development Program, PRI/ Dyncorp, National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, Maryland, 21702, USA

    Michael W. Smith

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Smith, M., Holmsen, A., Wei, Y. et al. Genomic sequence sampling: a strategy for high resolution sequence–based physical mapping of complex genomes. Nat Genet 7, 40–47 (1994). https://doi.org/10.1038/ng0594-40

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