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Nucleic Acids Research, 1990, Vol. 18, No. 21 6261-6270
© 1990

GENOME STRUCTURE AND MAPPING

Towards a physical map of the Drosophila melanogaster genome: mapping of cosmid clones within defined genomic divisions

I. Sidén-Kiamos1, R.D.C. Saunders2, L. Spanos1, T. Majerus3, J. Treanear3, C. Savakis1, C. Louis1, D.M. Glover2, M. Ashburner3 and F.C. Kafatos1,4

1Institute of Molecular Biology and Biotechnology, Research Center of Crete PO Box 1527, Heraklion 711 10, Crete, Greece 2Cancer Research Campaign Laboratories, Department of Biochemistry, University of Dundee Dundee DD1 4HN 3Department of Genetics, Cambridge University Downing Street, Cambridge CB2 3EH, UK 4Department of Cellular and Developmental Biology, Harvard University 16 Divinity Avenue, Cambridge, MA 02138, USA

Received July 30, 1990. Revised September 11, 1990. Accepted September 11, 1990.

A physical map of the D. melanogaster genome is being constructed, in the form of overlapping cosmid clones that are assigned to specific poiytene chromosome sites. A master library of Ca. 20,000 cosmids is screened with probes that correspond to numbered chromosomal divisions (ca. 1% of the genome); these probes are prepared by microdissection and PCRamplification of individual chromosomes. The 120 to 250 cosmids selected by each probe are fingerprinted by Hinfl digestion and gel electrophoresis, and overlaps are detected by computer analysis of the fingerprints, permitting us to assemble sets of contiguous clones (contigs). Selected cosmids, both from contlgs and unattached, are then localized by in situ hybridization to polytene chromosomes. Crosshybrldlzation analysIs using end probes links some contigs, and hybridization to previously cloned genes relates the physical to the genetic map. This approach has been used to construct a physical map of the 3.8 megabase DNA in the three distal divisions of the x chromosome. The map is represented by 181 canonical cosmids, of which 108 clones in contigs and 32 unattached clones have been mapped Individually by in situ hybridization to chromosomes. Our current database of in situ hybridization results also includes the beginning of a physical map for the rest of the genome: 162 cosmids have been assigned by In situ hybridization to 129 chromosomal subdivisions elsewhere in the genome, representing 5 to 6 megabases of additional mapped DNA.


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