For the first time, molecular biologists have established landmarks throughout the genome of one of the world's deadliest parasites, Plasmodium falciparum, which causes malaria and kills about 2 million people around the world each year. In today's Nature Genetics, researchers report that they have produced a so-called optical map of the parasite's 14 chromosomes, an achievement that should aid the ongoing effort to sequence the Plasmodium genome.
P. falciparum is a top target of gene sequencers because it has thwarted all attempts at control. There's no preventive vaccine, and in the past 2 decades the organism has become resistant to key antimalarial drugs. By sequencing its genome, researchers hope they will discover new ways to combat malaria. This effort involves first generating lots of tiny, overlapping bits of DNA that must be assembled in the right order after their nucleotide sequences are determined. The optical map, generated by David Schwartz of the University of Wisconsin, Madison, and his colleagues, should help in that assembly.
Schwartz developed optical mapping while he was at New York University. The technique takes advantage of electrostatic forces to stretch a taut piece of DNA onto a glass microscope slide. Then Schwartz and his colleagues treat the DNA with enzymes, each of which slices it only at certain strings of bases. As each enzyme cuts, the sizes of the resulting fragments, which are all lined up in the right order, are measured with digital imaging. A sophisticated computer program then weaves together a picture of the DNA, showing the sites nicked by each enzyme, which are the landmarks on the optical map.
Schwartz's team originally used the method to map single chromosomes, including chromosome 2 of P. falciparum, but has now developed computer software powerful enough to decipher fragments from all the parasite's chromosomes at once, thereby bypassing the need to first sort that DNA into separate chromosomes. "All we need is a tube of DNA and we're off," he adds.
Ultimately, sequencers can use the locations of the cuts to figure out where along the parasite's genome the newly sequenced DNA belongs. Optical mapping is "an incredibly fast and accurate way to authenticate the assembly" of pieces of sequence into a complete chromosome, says Leda Cummings, a molecular biologist who is sequencing part of the malarial genome at The Institute for Genomic Research in Rockville, Maryland. Indeed, with this and other maps, an international team of sequencers expects to finish the malarial genome by the end of 2001.