Plant Genome III Conference Plant Genome III Conference
The Lawrence Livermore National Laboratory (LLNL) has recently announced the completion of a high-resolution physical map of human chromosome 19. A vast amount of informatics expertise was gained in this process, all of which could be easily applied to large-scale physical mapping of various plant genomes. We will discuss a fully-automated physical mapping software procedure for integrating all the physical mapping data we have obtained by a variety of methods. The basis of our chromosome 19 physical mapping has been 15,000 cosmid clones which have been automatically assembled into 850 contigs. (Currently these procedures are being adapted for PAC and BAC clones to take advantage of the larger insert size.) We have used EcoRl restriction maps, metaphase and sperm pronuclei FISH mapping, cosmid walking, and many types of YAC/BAC/PAC <-> cosmid hybridizations to verify, order, and link our 850 contigs. We have developed a fully-automatic method of integrating these diverse data into a map that democratically clusters the data as a collection of ordered probes intersecting with various large "objects" (i.e., contigs, YACs, PACs, BACs, restriction maps) with length and distance information suppressed. Such a map has proved vital to us in discovering conflicts and errors, as well as guiding us to the most effective ways to achieve closure in each sub-region. We use a simulated annealing procedure that runs in 6 hours on our network of 45 workstations to integrate the data from some 4,200 probes and 1,000 larger objects. This yields a map which only shows order; a subsequent automated process adds in all length and distance data and performs map layout while minimizing conflicts. We have developed an extensive database and graphical browser interface to support these automated mapping tools. Although the software we have developed is highly tuned to our local needs and idiosyncracies, it is now being expanded to handle the mapping needs at LLNL on other genomic real estate and could be adapted to aid physical mapping of any organism. (This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory Contract No. W-7405-Eng- 48.)