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A shotgun optical map of the entire Plasmodium falciparum genome

Abstract

The 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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Figure 1: Schematic of shotgun optical mapping approach.
Figure 2: Digital fluorescence micrograph and map of a typical genomic DNA molecule.
Figure 3: High-resolution optical mapping of the P. falciparum genome using NheI and BamHI.
Figure 4: Identification of chromosomes and alignment of NheI and BamHI maps by mapping chromosome-specific YAC clones.

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Acknowledgements

We thank D. Lawson and T. Wellems for clones and other valuable reagents. This work was supported by the Burroughs Wellcome Fund, NIH, and the Naval Medical Research and Development Command work unit STEP C611102A0101BCX. Additional support came from NCHGR (2 RO1 HG00225-01-09) and NCI1(RO1CA 79063-1).

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Correspondence to David C. Schwartz.

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Lai, Z., Jing, J., Aston, C. et al. A shotgun optical map of the entire Plasmodium falciparum genome. Nat Genet 23, 309–313 (1999). https://doi.org/10.1038/15484

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