Optical mapping of Plasmodium falciparum chromosome 2

Detailed restriction maps of microbial genomes are a valuable resource in g enome sequencing studies but are toilsome to construct by contig constructi on of maps derived from cloned DNA. Analysis of genomic DNA enables large s tretches of the genome to be mapped and circumvents library construction an d associated cloning artifacts. We used pulsed-field gel electrophoresis pu rified Plasmodium falciparum chromosome 2 DNA as the starting material for optical mapping, a system for making ordered restriction maps from ensemble s of individual DNA molecules. DNA molecules were bound to derivatized glas s surfaces, cleaved with NheI or BamHI, and imaged by digital Fluorescence microscopy. Large pieces of the chromosome containing ordered DNA restricti on fragments were mapped. Maps were assembled from 50 molecules producing a n average contig depth of 15 molecules and high-resolution restriction maps covering the entire chromosome. Chromosome 2 was found to be 976 kb by opt ical mapping with Nhel, and 946 kb with BamHI, which compares closely to th e published size of 947 kb from large-scale sequencing. The maps were used to further verify assemblies from the plasmid library used for sequencing. Maps generated in silico from the sequence data were compared to the optica l mapping data, and good correspondence was found. Such high-resolution res triction maps may become an indispensable resource for large-scale genome s equencing projects.