Skip to main content
SpringerLink
Log in

Drosophila genome project: One-hit coverage in yeast artificial chromosomes

  • Original Articles
  • Published:
Chromosoma Aims and scope Submit manuscript

Abstract

We present a strategy for assembling a physical map of the genome of Drosophila melanogaster based on yeast artificial chromosomes (YACs). In this paper we report 500 YACs containing inserts of Drosophila DNA averaging 200 kb that have been assigned positions on the physical map by means of in situ hybridization with salivary gland chromosomes. The cloned DNA fragments have randomly sheared ends (DY clones) or ends generated by partial digestion with either NotI (N clones) or EcoRI (E clones). Relative to the euchromatic portion of the genome, the size distribution and genomic positions of the clones reveal no significant bias in the completeness or randomness of genome coverage. The 500 mapped euchromatic clones contain an aggregate of approximately 100 million base pairs of DNA, which is approximately one genome equivalent of Drosophila euchromatin.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Ashburner, M (1989) Drosophila: A laboratory handbook. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York

    Google Scholar 

  • Bender, W, Spierer, P, Hogness, DS (1983) Chromosome walking and jumping to isolate DNA from the Ace and rosy loci and the Bithorax complex in Drosophila melanogaster. J Mol Biol 168: 17–33

    Google Scholar 

  • Bingham, PM, Levis, R, Rubin, GM (1981) Cloning of DNA sequences from the white locus of Drosophila melanogaster by a novel and general method. Cell 25: 693–704

    Google Scholar 

  • Bingham, PM, Kidwell, MG, Rubin, GM (1982) The molecular basis of P-M hybrid dysgenesis: the role of the P element, a P-strain specific transposon family. Cell 29: 995–1004

    Google Scholar 

  • Bridges, CM (1935) Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. J Hered 26: 60–64

    Google Scholar 

  • Burke, DT, Carle, GF, Olson, MV (1987) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236: 806–812

    Google Scholar 

  • Capecchi, M (1990) How efficient can you get? Nature 348: 109

    Google Scholar 

  • Carle, GF, Olson, MV (1984) Separation of chromosomal DNA molecules from yeast by orthogonal-field-alternation gel electrophoresis. Nucleic Acids Res 12: 5647–5663

    Google Scholar 

  • Clayton, FE, Guest, WC (1986) Overview of chromosomal evolution in the family Drosophilidae. In: Ashburner, M, Carson, HL, Thompson, JNJ (eds) Genetics and biology of Drosophila. Academic Press, New York, pp 1–38

    Google Scholar 

  • Cooley, L, Kelley, R, Spradling, A (1988) Insertional mutagenesis of the Drosophila genome with single P elements. Science 239: 1121–1128

    Google Scholar 

  • Coulson, A, Sulston, J, Brenner, S, Karn, J (1986) Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci USA 83: 7821–7825

    Google Scholar 

  • Coulson, A, Waterston, R, Kiff, J, Sulston, J, Kohara, Y (1988) Genome linking with yeast artificial chromosomes. Nature 335: 184–186

    Google Scholar 

  • Craig, AG, Nizetic, D, Hoheisel, JD, Zehetner, G, Lehrach, H (1990) Ordering of cosmid clones covering Herpes simplex virus type I (HSV-I) genome: a test case for fingerprinting by hybridization. Nucleic Acids Res 18: 2653–2660

    Google Scholar 

  • Danilevskaya, ON, Kurenova, EV, Pavlova, MN, Link, AJ, Koga, A, Vellek, A, Hartl, DL (1991) He-T family DNA sequences in the Y chromosome of Drosophila melanogaster share homology with the X-linked Stellate genes. Chromosoma 100: 118–124

    Google Scholar 

  • Feinberg, AP, Vogelstein, B (1984) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity: Addendum. Anal Biochem 137: 266–267

    Google Scholar 

  • Feller, W (1950) An introduction to probability theory and its applications. John Wiley, New York

    Google Scholar 

  • Garza, D, Ajioka, JW, Burke, DT, Hartl, DL (1989a) Mapping the Drosophila genome with yeast artificial chromosomes. Science 246: 641–646

    Google Scholar 

  • Garza, D, Ajioka, JW, Carulli, JP, Jones, RW, Johnson, DH, Hartl, DL (1989b) Physical mapping of complex genomes. Nature 340: 577–578

    Google Scholar 

  • Green, ED, Olson, MV (1990) Systematic screening of yeast artificial-chromosome libraries by use of the polymerase chain reaction. Proc Natl Acad Sci USA 87: 1213–1217

    Google Scholar 

  • Healy, MJ, Russell, RJ, Miklos, GLG (1988) Molecular studies on interspersed repetitive and unique sequences in the region of the complementation group uncoordinated on the X chromosome of Drosophila melanogaster. Mol Gen Genet 213: 63–71

    Google Scholar 

  • Johnson, DH (1990) Molecular cloning of DNA from specific chromosomal regions by microdissection and sequence-independent amplification of DNA. Genomics 6: 243–251

    Google Scholar 

  • Kohara, Y, Akiyama, K, Isono, K (1987) The physical map of the whole E. coli chromosome: Application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50: 495–508

    Google Scholar 

  • Langer-Safer, PR, Levine, M, Ward, DC (1982) Immunological method for mapping genes on Drosophila polytene chromosomes. Proc Natl Acad Sci USA 79: 4381–4385

    Google Scholar 

  • Lefevre, GJr (1976) A photographic representation and interpretation of the polytene chromosomes of Drosophila melanogaster savary glands. In: Ashburner, M, Novitski, E (eds) The genetics and biology of Drosophila. Academic Press, New York, pp 31–66

    Google Scholar 

  • Lindsley, DL, Zimm, G (1985) The genome of Drosophila melanogaster. Part 1: Genes A-K. Dros Inf Serv 62: 1–227

    Google Scholar 

  • Lindsley, DL, Zimm, G (1986) The genome of Drosophila melanogaster. Part 2: lethals; maps. Dros Inf Serv 64: 1–158

    Google Scholar 

  • Lindsley, DL, Zimm, G (1987) The genome of Drosophila melanogaster. Part 3: rearrangements. Dros Inf Serv 65: 1–224

    Google Scholar 

  • Lindsley, DL, Zimm, G (1990) The genome of Drosophila melanogaster. Part 4: Genes L-Z. Dros Inf Sery 68: 1–382

    Google Scholar 

  • Ochman, H, Gerber, AS, Hartl, DL (1988) Genetic applications of an inverse polymerase chain reaction. Genetics 120: 621–623

    Google Scholar 

  • Ochman, H, Medhora, MM, Garza, D, Hartl, DL (1990) Amplification of flanking sequences by inverse PCR. In: Innis, M, Gelfand, D, Sninsky, J, White, T (eds) PCR protocols: A guide to methods and applications. Academic Press, New York, pp 219–227

    Google Scholar 

  • Olson, MV, Dutchik, JE, Graham, MY, Brodeur, GM, Helms, C, Frank, M, MacCollin, M, Scheinman, R, Frank, T (1986) Random-clone strategy for genomic restriction mapping in yeast. Proc Natl Acad Sci USA 83: 7826–7830

    Google Scholar 

  • Olson, MV, Hood, L, Cantor, C, Botstein, D (1989) A common language for physical mapping of the human genome. Science 245: 1434–1440

    Google Scholar 

  • Painter, TS (1933) A new method for the study of chromosome rearrangements and the plotting of chromosome maps. Science 78: 585–586

    Google Scholar 

  • Palazzolo, MJ, Hyde, DR, VijayRaghavan, K, Mecklenberg, K, Benzer, S, Meyerowitz, E (1989) Use of a new strategy to isolate and characterize 436 Drosophila cDNA clones corresponding to RNAs detected in adult heads but not early embryos. Neuron 3: 527–539

    Google Scholar 

  • Pfeifer, GP, Steigerwald, SD, Mueller, PR, Wold, B, Riggs, AD (1989) Genomic sequencing and methylation analysis by ligation mediated PCR. Science 246: 810–813

    Google Scholar 

  • Riethman, HC, Moyzis, RK, Meyne, J, Burke, DT, Olson, MV (1989) Cloning human telomeric DNA fragments into Saccharomyces cerevisiae using a yeast-artificial-chromosome vector. Proc Natl Acad Sci USA 86: 6240–6244

    Google Scholar 

  • Riley, J, Butler, R, Ogilvie, D, Finniear, R, Jenner, D, Powell, S, Anand, R, Smith, JC, Markham, AF (1990) A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids Res 18: 2887–2890

    Google Scholar 

  • Rubin, GM, Spradling, AC (1982) Genetic transformation of Drosophila with transposable element vectors. Science 218: 348–353

    Google Scholar 

  • Rudkin, GT (1969) Non replicating DNA in Drosophila. Genetics 61 [Suppl 1]: 227–238

    Google Scholar 

  • Saunders, RDC, Glover, DM, Ashburner, M, Siden-Kiamos, I, Louis, C, Monastirioti, M, Savakis, C, Kafatos, F (1989) PCR amplification of DNA microdissected from a single polytene chromosome band: a comparison with conventional microcloning. Nucleic Acids Res 17: 9027–9037

    Google Scholar 

  • Scott, MP, Weiner, AJ, Polisky, BA, Hazelrigg, TI, Pirrotta, V, Scalenghe, F, Kaufman, TC (1983) The molecular organization of an Antennapedia locus of Drosophila. Cell 35: 763–776

    Google Scholar 

  • Siden-Kiamos, I, Saunders, RDC, Spanos, L, Majerus, T, Treanear, J, Savakis, C, Louis, C, Glover, DM, Ashburner, M, Kafatos, FC (1990) Towards a physical map of the Drosophila melanogaster genome: Mapping of cosmid clones within defined genomic divisions. Nucleic Acids Res 18: 6261–6270

    Google Scholar 

  • Smoller, D, Petrov, D, Hartl, DL (1991) Characterization of bacteriophage P1 library containing inserts of Drosophila DNA of 75–100 kilobase pairs. Chromosoma 100: 487–494

    Google Scholar 

  • Sorsa, V (1988a) Chromosome maps of Drosophila, vol I. CRC Press, Boca Raton, Florida

    Google Scholar 

  • Sorsa, V (1988b) Chromosoma maps of Drosophila, vol II. CRC Press, Boca Raton, Florida

    Google Scholar 

  • Southern, EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98: 503–517

    Google Scholar 

  • Steller, H, Pirrotta, V (1985) A transposable P vector that confers selectable G418 resistance to Drosophila larvae. EMBO J 4: 167–171

    Google Scholar 

  • Sternberg, N (1990) Bacteriophage P1 cloning system for the isolation, amplification, and recovery of DNA fragments as large as 100 kilobase pairs. Proc Natl Acad Sci USA 87: 103–107

    Google Scholar 

  • Sturtevant, AH (1913) The linear arrangement of six sex-linked genes in Drosophila, as shown by their mode of association. J Exp Zool 14: 43–59

    Google Scholar 

  • Vogelstein, B, Gillespie, D (1979) Preparative and analytical purification of DNA from agarose. Proc Natl Acad Sci USA 76: 615–619

    Google Scholar 

  • Vollrath, D, Davis, RW (1987) Resolution of DNA molecules greater than 5 megabases by contour-clamped homogeneous electric fields. Nucleic Acids Res 15: 7865–7876

    Google Scholar 

Download references

Author information

Author notes

  1. James W. Ajioka

    Present address: London School of Hygiene and Tropical Medicine, London, UK

  2. Dan Garza

    Present address: Department of Development Biology, Stanford University, Stanford, CA, USA

Authors and Affiliations

  1. Department of Genetics, Washington University School of Medicine, 63110-1095, St. Louis, MO, USA

    James W. Ajioka, David A. Smoller, Robert W. Jones, John P. Carulli, Ann E. C. Vellek, Dan Garza, Ian W. Duncan & Daniel L. Hartl

  2. Department of Genetics, Harvard Medical School, 02115, Boston, MA, USA

    Andrew J. Link

  3. Department of Biology, Washington University, 63130, St. Louis, MC, USA

    Ian W. Duncan

Authors
  1. James W. Ajioka
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David A. Smoller
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Robert W. Jones
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. John P. Carulli
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ann E. C. Vellek
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Dan Garza
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Andrew J. Link
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ian W. Duncan
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Daniel L. Hartl
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

by W. Hennig

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ajioka, J.W., Smoller, D.A., Jones, R.W. et al. Drosophila genome project: One-hit coverage in yeast artificial chromosomes. Chromosoma 100, 495–509 (1991). https://doi.org/10.1007/BF00352200

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00352200

Keywords

Search

Navigation