A YEAST ARTIFICIAL CHROMOSOME CLONE MAP OF THE DROSOPHILA GENOME

We describe the mapping of 979 randomly selected large yeast artificia l chromosome (YAC) clones of Drosophila DNA by in situ hybridization t o polytene chromosomes. Eight hundred and fifty-five of the clones are euchromatic and have primary hybridization sites in the banded portio ns of the polytene chromosomes, whereas 124 are heterochromatic and la bel the chromocenter. The average euchromatic clone contains about 211 kb and, at its primary site, labels eight or nine contiguous polytene bands. Thus, the extent as well as chromosomal position of each clone has been determined. By direct band counts, we estimate our clones pr ovide about 76% coverage of the euchromatin of the major autosomes, an d 63% coverage of the X. When previously reported YAC mapping data are combined with ours, euchromatic coverage is extended to about 90% for the autosomes and 82% for the X. The distribution of gap sizes in our map and the coverage achieved are in good agreement with expectations based on the assumption of random coverage, indicating that euchromat ic clones are essentially randomly distributed. However, certain gaps in coverage, including the entire fourth chromosome euchromatin, may b e significant. Heterochromatic sequences are underrepresented among th e YAC clones by two to three fold. This may result, at least in part, from underrepresentation of heterochromatic sequences in adult DNA (th e source of most of the clones analyzed), or from clone instability.