GENOME PROPERTIES AND THEIR INFLUENCES ON LIBRARY CONSTRUCTION AND PHYSICAL MAPPING

Dept of Soil & Crop Sciences, 2474 Texas A & M University, College Station,TX 77843-2474

(*Co-senior author; **Correspinding author) BAC libraries and physical maps are crucial to modern genome research. To study the influences of genome property on BAC library construction and genome physical mapping, we conducted a simulated study with three sequence-known chromosomes, Arabidopsis chromosome 4, a random chromosome containing a repeated region, and a random chromosome consisting of regions with A/T contents varying from 45 to 70%. DNA was partially digested with Hind III, Bam HI and EcoRI, respectively, and libraries with the insertion of 140 -160 kb were constructed. Clones were fingerprinted and contigs assembled with FPC. Results showed that the distribution patterns of restriction sites for the three enzymes along each chromosome were dramatically different. In different regions of a chromosome, the restriction site frequency of an enzyme could vary by 30 fold. The abundance of clones constructed along each chromosome was significantly correlated with the restriction site frequency, and its distribution tended to be even for the library constructed with three different enzymes. The gaps of the physical map constructed from a single-enzyme library was more than 5 times as many as that from a three-enzyme library having the same genome coverage. Results also showed that large repeat segments could make clones from the region pile up in a contig and the clones from neighboring regions questionable clones (Qs). To make a better genome coverage library and physical map, it is always recommended to use two or more enzymes that are complementary in restriction site base composition in library construction.