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

Article metrics

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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 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)

  2. 2

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

  3. 3

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

  4. 4

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

  5. 5

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

  6. 6

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

  7. 7

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

  8. 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)

  9. 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)

  10. 10

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

  11. 11

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

  12. 12

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

  13. 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)

  14. 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)

  15. 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)

  16. 16

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

  17. 17

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

  18. 18

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

  19. 19

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

  20. 20

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

  21. 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)

  22. 22

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

  23. 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)

  24. 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)

  25. 25

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

  26. 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)

  27. 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)

  28. 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)

  29. 29

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

  30. 30

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

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.

Author information

Correspondence to Malcolm J. Gardner.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.