Sequence of Plasmodium falciparum chromosome 12

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Abstract

The human malaria parasite Plasmodium falciparum is responsible for the death of more than a million people every year1. To stimulate basic research on the disease, and to promote the development of effective drugs and vaccines against the parasite, the complete genome of P. falciparum clone 3D7 has been sequenced, using a chromosome-by-chromosome shotgun strategy2,3,4. Here we report the nucleotide sequence of the third largest of the parasite's 14 chromosomes, chromosome 12, which comprises about 10% of the 23-megabase genome. As the most (A + T)-rich (80.6%) genome sequenced to date, the P. falciparum genome presented severe problems during the assembly of primary sequence reads. We discuss the methodology that yielded a finished and fully contiguous sequence for chromosome 12. The biological implications of the sequence data are more thoroughly discussed in an accompanying Article (ref. 3).

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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

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

  3. 3

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

  4. 4

    Gardner, M. J. et al. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature 419, 531–534 (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

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

  7. 7

    Rubio, J. P., Thompson, J. K. & Cowman, A. F. The var genes of Plasmodium falciparum are located in the subtelomeric region of most chromosomes. EMBO J. 15, 4069–4077 (1996)

  8. 8

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

  9. 9

    Su, X. Z. & Wellems, T. E. Plasmodium falciparum: assignment of microsatellite markers to chromosomes by PFG-PCR. Exp. Parasitol. 91, 367–369 (1999)

  10. 10

    Jing, J. et al. Optical mapping of Plasmodium falciparum chromosome 2. Genome Res. 9, 175–181 (1999)

  11. 11

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

  12. 12

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

  13. 13

    Ewing, B. & Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194 (1998)

  14. 14

    Oefner, P. J. et al. Efficient random subcloning of DNA sheared in a recirculating point-sink flow system. Nucleic Acids Res. 24, 3879–3886 (1996)

  15. 15

    Ewing, B., Hillier, L., Wendl, M. C. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185 (1998)

  16. 16

    Gordon, D., Abajian, C. & Green, P. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202 (1998)

  17. 17

    Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)

  18. 18

    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)

  19. 19

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

  20. 20

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

  21. 21

    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)

  22. 22

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

  23. 23

    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)

  24. 24

    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)

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Acknowledgements

We acknowledge the generosity of the participating scientists at Stanford University, TIGR, the WTSI, the NMRC and Oxford University. We also thank N. Hall, M. Berriman, A. Pain and B. Barrell for their time and expertise during the gene-calling annotation process, and are grateful to the members of our Stanford Genome Technology Center for their assistance throughout this project. We thank the Burroughs Wellcome Fund for support that allowed us to participate in the international Malaria Genome Project.

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Correspondence to Richard W. Hyman.

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The authors declare that they have no competing financial interests.

Supplementary information

Supplementary figure 1 (PDF 220 kb)

Supplementary figure 2 (PDF 418 kb)

Legends for supplementary figures 1 and 2 (DOC 19 kb)

Supplementary tables (DOC 30 kb)

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