A physical map of the 31-megabase Aspergillus nidulans genome is reported, in which 94% of 5,134 cosmids are assigned to 49 contiguous segments. The physical map is the result of a two-way ordering process, in which clones and probes were ordered simultaneously on a binary DNA͞DNA hybridization matrix. Compression by elimination of redundant clones resulted in a minimal map, which is a chromosome walk. Repetitive DNA is nonrandomly dispersed in the A. nidulans genome, reminiscent of heterochromatic banding patterns of higher eukaryotes. We hypothesize gene clusters may arise by horizontal transfer and spread by transposition to explain the nonrandom pattern of repeats along chromosomes.The ascomycetous fungus Aspergillus nidulans is one of the simplest multicellular eukaryotes. Its estimated 31-megabase genome (1) with low repetitive DNA content (2), distributed among eight chromosomes, is sufficiently complex to direct multicellular development (3, 4). With its sophisticated forward and reverse genetics (5, 6), A. nidulans has been used to address fundamental questions in cell and molecular biology (7-10) and has become a model system for the study of pathogenic and biotechnologically useful relatives (11, 12). One of the major questions in genomics is the organization of repeated DNA sequences in a genome because this organization has implications for functional organization of genomes, development, chromosome structure and function, recombination, and genome evolution. Small eukaryotic genomes provide excellent models for the development of novel mapping technologies for larger genomes. For example, the A. nidulans genome is entirely covered (tiled) by 775 nonoverlapping cosmids (averaging Ϸ40-kb inserts) and the human genome, with 3,000 yeast artificial chromosomes [averaging Ϸ1,001-kb inserts, (13)]. Here we present a physical mapping strategy that produces a portrait of how repeated DNA sequences are distributed in small eukaryotic genomes.
MATERIALS AND METHODSLibraries. Two independent libraries were constructed in the Lambda-based cosmid vector pLORIST2 and the pBRbased cosmid vector pWE15 (1).Physical Mapping Strategy. For the physical mapping experiment, pulsed field gel electrophoresis isolated chromosomes were radiolabeled and used, one by one, to probe the two genomic libraries (5,134 clones stamped onto seven highdensity gridded 5 ϫ 3.5-inch nylon membranes containing 864 clones each) to show the chromosomal affiliations of each clone (1). With this information, clones were sorted into subsets (S for specific to one chromosome, R for repeated hybridization to several, but not all, chromosomes, and O for octochromosomal). Octochromosomal (O) clones hybridized to all eight A. nidulans chromosomes. The numbers of S, R, and O clones in the genomic library were 3,307 (64.4%), 1,769 (34.4%), and 58 (1.1%), respectively. Then, only S clones were radiolabeled and used to probe the genomic library of 5,134 clones (on seven identical membranes)