Nature Genetics
23, 309 - 313 (1999)
doi:10.1038/15484
A shotgun optical map of the entire Plasmodium falciparum genomeZhongwu Lai1, Junping Jing1, Christopher Aston1, Virginia Clarke1, Jennifer Apodaca1, Eileen T. Dimalanta1, Daniel J. Carucci3, Malcolm J. Gardner4, Bud Mishra2, Thomas S. Anantharaman2, Salvatore Paxia2, Stephen L. Hoffman3, J. Craig Venter4, Edward J. Huff1
& David C. Schwartz1, 51
W.M. Keck Laboratory for Biomolecular Imaging, Department of Chemistry and
2
Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, Department of Chemistry, New York, New York, USA. 3
Malaria Program, Naval Medical Research Center and
4
The Institute for Genomic Research, Rockville, Maryland, USA. 5
Present address: University of Wisconsin-Madison, Departments of Chemistry and Genetics, UW Biotechnology Center, Madison, Wisconsin, USA.
Correspondence should be addressed to David C. Schwartz schwad01@mcrcr.med.nyu.eduThe unicellular parasite Plasmodium falciparum is the cause of human malaria, resulting in 1.7−2.5 million deaths each year1. To develop new means to treat or prevent malaria, the Malaria Genome Consortium was formed to sequence and annotate the entire 24.6-Mb genome2. The plan, already underway, is to sequence libraries created from chromosomal DNA separated by pulsed-field gel electrophoresis (PFGE). The AT-rich genome of P. falciparum presents problems in terms of reliable library construction and the relative paucity of dense physical markers or extensive genetic resources. To deal with these problems, we reasoned that a high-resolution, ordered restriction map covering the entire genome could serve as a scaffold for the alignment and verification of sequence contigs developed by members of the consortium. Thus optical mapping was advanced to use simply extracted, unfractionated genomic DNA as its principal substrate. Ordered restriction maps (BamHI and NheI) derived from single molecules were assembled into 14 deep contigs corresponding to the molecular karyotype determined by PFGE (ref. 3).
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