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Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14

Abstract

The mosquito-borne malaria parasite Plasmodium falciparum kills an estimated 0.7–2.7 million people every year, primarily children in sub-Saharan Africa. Without effective interventions, a variety of factors—including the spread of parasites resistant to antimalarial drugs and the increasing insecticide resistance of mosquitoes—may cause the number of malaria cases to double over the next two decades1. To stimulate basic research and facilitate the development of new drugs and vaccines, the genome of Plasmodium falciparum clone 3D7 has been sequenced using a chromosome-by-chromosome shotgun strategy2,3,4. We report here the nucleotide sequences of chromosomes 10, 11 and 14, and a re-analysis of the chromosome 2 sequence5. These chromosomes represent about 35% of the 23-megabase P. falciparum genome.

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References

  1. Breman, J. G. The ears of the hippopotamus: manifestations, determinants, and estimates of the malaria burden. Am. J. Trop. Med. Hyg. 64, 1–11 (2001)

    CAS  Article  Google Scholar 

  2. Gardner, M. J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498–511 (2002)

    ADS  CAS  Article  Google Scholar 

  3. Hall, N. et al. Sequence of Plasmodium falciparum chromosomes 1, 3–9 and 13. Nature 419, 527–531 (2002)

    ADS  CAS  Article  Google Scholar 

  4. Hyman, R. W. et al. Sequence of Plasmodium falciparum chromosome 12. Nature 419, 534–537 (2002)

    ADS  CAS  Article  Google Scholar 

  5. Gardner, M. J. et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 282, 1126–1132 (1998)

    ADS  CAS  Article  Google Scholar 

  6. Glockner, G. et al. Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature 418, 79–85 (2002)

    ADS  Article  Google Scholar 

  7. Bowman, S. et al. The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature 400, 532–538 (1999)

    ADS  CAS  Article  Google Scholar 

  8. Cawley, S. E., Wirth, A. I. & Speed, T. P. Phat—a gene finding program for Plasmodium falciparum. Mol. Biochem. Parasitol. 118, 167–174 (2001)

    CAS  Article  Google Scholar 

  9. Salzberg, S. L., Pertea, M., Delcher, A., Gardner, M. J. & Tettelin, H. Interpolated Markov models for eukaryotic gene finding. Genomics 59, 24–31 (1999)

    CAS  Article  Google Scholar 

  10. Huestis, R. & Fischer, K. Prediction of many new exons and introns in Plasmodium falciparum chromosome 2. Mol. Biochem. Parasitol. 118, 187–199 (2001)

    CAS  Article  Google Scholar 

  11. Maniatis, T. & Tasic, B. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418, 236–243 (2002)

    ADS  CAS  Article  Google Scholar 

  12. Lawrence, C. E. et al. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262, 208–214 (1993)

    ADS  CAS  Article  Google Scholar 

  13. Ramchatesingh, J., Zahler, A. M., Neugebauer, K. M., Roth, M. B. & Cooper, T. A. A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer. Mol. Cell Biol. 15, 4898–4907 (1995)

    CAS  Article  Google Scholar 

  14. Fairbrother, W. G., Yeh, R. F., Sharp, P. A. & Burge, C. B. Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007–1013 (2002)

    ADS  CAS  Article  Google Scholar 

  15. Walliker, D., Quayki, I., Wellems, T. E. & McCutchan, T. F. Genetic analysis of the human malaria parasite Plasmodium falciparum. Science 236, 1661–1666 (1987)

    ADS  CAS  Article  Google Scholar 

  16. Foster, J. & Thompson, J. The Plasmodium falciparum genome project: a resource for researchers. Parasitol. Today 11, 1–4 (1995)

    Article  Google Scholar 

  17. Su, X. et al. A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum. Science 286, 1351–1353 (1999)

    CAS  Article  Google Scholar 

  18. Lai, Z. et al. A shotgun optical map of the entire Plasmodium falciparum genome. Nature Genet. 23, 309–313 (1999)

    CAS  Article  Google Scholar 

  19. Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 30, 276–280 (2002)

    CAS  Article  Google Scholar 

  20. Falquet, L. et al. The PROSITE database, its status in 2002. Nucleic Acids Res. 30, 235–238 (2002)

    CAS  Article  Google Scholar 

  21. Apweiler, R. et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29, 37–40 (2001)

    CAS  Article  Google Scholar 

  22. Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nature Genet. 25, 25–29 (2000)

    CAS  Article  Google Scholar 

  23. Nielsen, H., Engelbrecht, J., Brunak, S. & von Heijne, G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10, 1–6 (1997)

    CAS  Article  Google Scholar 

  24. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001)

    CAS  Article  Google Scholar 

  25. Claros, M. G. & Vincens, P. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241, 779–786 (1996)

    CAS  Article  Google Scholar 

  26. Emanuelsson, O., Nielsen, H., Brunak, S. & von Heijne, G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300, 1005–1016 (2000)

    CAS  Article  Google Scholar 

  27. Zuegge, J., Ralph, S., Schmuker, M., McFadden, G. I. & Schneider, G. Deciphering apicoplast targeting signals—feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins. Gene 280, 19–26 (2001)

    CAS  Article  Google Scholar 

  28. Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997)

    CAS  Article  Google Scholar 

  29. Florens, L. et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520–526 (2002)

    ADS  CAS  Article  Google Scholar 

  30. Lasonder, E. et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419, 537–542 (2002)

    ADS  CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank our colleagues at The Institute for Genomic Research and the Naval Medical Research Center for support; J. Foster for providing markers for chromosome 14; R. Huestis and K. Fischer for providing RT–PCR data for chromosomes 2 and 3 before publication; and S. Cawley for assistance with phat. This work was supported by the Burroughs Wellcome Fund, the National Institute for Allergy and Infectious Diseases, the Naval Medical Research Center, and the US Army Medical Research and Materiel Command.

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Correspondence to Malcolm J. Gardner.

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Gardner, M., Shallom, S., Carlton, J. et al. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature 419, 531–534 (2002). https://doi.org/10.1038/nature01094

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