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).
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
World Health Organization. World malaria situation in 1994. Part I. Population at risk. Wkly Epidemiol. Rec. 72, 269–274 (1997).
Wirth, D. Malaria: a 21st century solution for an ancient disease. Nature Med. 4, 1360–1362 (1998).
Schwartz, D.C. & Cantor, C.R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37, 67–75 (1984).
Cai, W., Aburatani, H., Housman, D., Wang, Y. & Schwartz, D.C. Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces. Proc. Natl Acad. Sci. USA 92, 5164–5168 (1995).
Cai, W. et al. High resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping. Proc. Natl Acad. Sci. USA 95, 3390–3395 (1998).
Jing, J. et al. Automated high resolution optical mapping using arrayed, fluid fixed, DNA molecules. Proc. Natl Acad. Sci. USA 95, 8046–8051 (1998).
Jing, J. et al. Optical mapping of Plasmodium falciparum chromosome 2. Genome Res. 9, 175–181 (1999).
Lin, J. et al. Whole genome shotgun optical mapping of Deinococcus radiodurans. Science 285, 1558–1562 (1999).
Schwartz, D.C. & Samad, A. Optical mapping approaches to molecular genomics. Curr. Opin. Biotechnol. 8, 70–74 (1997).
Meng, X., Benson, K., Chada, K., Huff, E.J. & Schwartz, D.C. Optical mapping of lambda bacteriophage clones using restriction endonucleases. Nature Genet. 9, 432–438 (1995).
Anantharaman, T.S., Mishra, B. & Schwartz, D.C. Genomics via Optical Mapping III: contiging genomic DNA and variations. in Courant Technical Report 760 (Courant Institute, New York University, New York, 1998).
Anantharaman, T.S., Mishra, B. & Schwartz, D.C. Genomics via Optical Mapping III: contiging genomic DNA and variations. The Seventh International Conference on Intelligent Systems for Molecular Biology 7, 18–27 (1999).
Gardner, M.J. et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 282, 1126–1132 (1998).
Pace, T., Ponzi, M., Scotti, R. & Frontali, C. Structure and superstructure of Plasmodium falciparum subtelomeric regions. Mol. Biochem. Parasitol. 69, 257–268 (1995).
Van der Ploeg, L.H.T., Schwartz, D.C., Cantor, C.R. & Borst, P. Antigenic variation in Trypanosoma brucei analyzed by electrophoretic separation of chromosome sized DNA molecules. Cell 37, 77–84 (1984).
Spithill, T.W. & Samaras, N. The molecular karyotype of Leishmania major and mapping of α and β tubulin gene families to multiple unlinked chromosomal loci. Nucleic Acid Res. 13, 4155–4169 (1985).
Ahamada, S., Wery, M. & Hamers, R. Rodent malaria parasites: molecular karyotypes characterize species, subspecies and lines. Parasite 1, 31–38 (1994).
Moritz, K.B. & Roth, G.E. Complexity of germline and somatic DNA in Ascaris. Nature 259, 55–57 (1976).
Fleischmann, R.D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512 (1995).
Fraser, C.M. et al. The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403 (1995).
Goffeau, A. et al. Life with 6000 genes. Science 274, 546, 563–567 (1996).
The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018 (1998).
Mullikin, J.C. & McMurray, A.A. Sequencing the genome, fast. Science 283, 1867–1868 (1999).
Venter, J.C. et al. Shotgun sequencing of the human genome. Science 280, 1540–1542 (1998).
Bowman, S. et al. The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature 400, 532–538 (1999).
Trager, W. & Jensen, J.B. Human malaria parasites in continuous culture. Science 193, 673–675 (1976).
Corcoran, L.M., Forsyth, K.P., Bianco, A.E., Brown, G.V. & Kemp, D.J. Chromosome size polymorphism in Plasmodium falciparum can involve deletions and are frequent in nature parasite populations. Cell 44, 87–95 (1986).
Aston, C., Hiort, C. & Schwartz, D.C. Optical mapping: an approach for fine mapping. Methods Enzymol. 303, 55–73 (1999).
Netzel, T.L., Nafisi, K., Zhao, M., Lenhard, J.R. & Johnson, I. Base-content dependence of emission enhancements, quantum yields, and lifetimes for cyanine dyes bound to double-strand DNA: photophysical properties of monomeric and bichromophoric DNA stains. J. Phys. Chem. 99, 17936–17947 (1995).
Schwartz, D.C. & Koval, M. Conformational dynamics of individual DNA molecules during gel electrophoresis. Nature 338, 520–522 (1989).
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).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/15484
This article is cited by
-
An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
Scientific Reports (2018)
-
DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle
Nature Communications (2017)
-
Rapid construction of genome map for large yellow croaker (Larimichthys crocea) by the whole-genome mapping in BioNano Genomics Irys system
BMC Genomics (2015)
-
A clone-free, single molecule map of the domestic cow (Bos taurus) genome
BMC Genomics (2015)
-
Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association
BMC Genomics (2012)