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Sequence of Plasmodium falciparum chromosomes 1, 3–9 and 13


Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum1,2, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3–9 and 13 of P. falciparum clone 3D7—these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts.

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Figure 1: Scatter graphs of virtual restriction digests of completed chromosomes and pseudo-chromosomes against optical map fragment sizes.
Figure 2: Comparison of the percentage of annotations with specific Gene Ontology terms on each chromosome.
Figure 3: Position and structure of var-related (G + C)-rich elements.


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We thank the staff in the computer support and software development groups; J. Thompson and A. Cowman for gifts of YAC clones and for advice; D. Schwartz for optical map data; X. Su for genetic map information; Y. Shaw for help with Fig. 1; M. Harris and M. Ashburner for assistance with the parasite specific GO terms; O. White and M. Gardner for Table 1 and supplementary figures; the other members of the Malaria Genome Sequencing Consortium for discussions; and The Wellcome Trust Plasmodium Genome Mapping Consortium. This work was supported by the Wellcome Trust.

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Correspondence to N. Hall.

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

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