Abstract
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.
This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Assessment of genetic diversity of Plasmodium falciparum circumsporozoite protein in Sudan: the RTS,S leading malaria vaccine candidate
Malaria Journal Open Access 10 November 2021
-
Genotyping cognate Plasmodium falciparum in humans and mosquitoes to estimate onward transmission of asymptomatic infections
Nature Communications Open Access 10 February 2021
-
Characterization of Plasmodium falciparum NEDD8 and identification of cullins as its substrates
Scientific Reports Open Access 19 November 2020
Access options
Subscribe to this journal
Receive 51 print issues and online access
$199.00 per year
only $3.90 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
References
Gardner, M. J. et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 282, 1126–1132 (1998)
Bowman, S. et al. The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature 400, 532–538 (1999)
Su, X. et al. A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum. Science 286, 1351–1353 (1999)
Lai, Z. et al. A shotgun optical map of the entire Plasmodium falciparum genome. Nature Genet. 23, 309–313 (1999)
de Bruin, D., Lanzer, M. & Ravetch, J. V. Characterization of yeast artificial chromosomes from Plasmodium falciparum: construction of a stable, representative library and cloning of telomeric DNA fragments. Genomics 14, 332–339 (1992)
Glockner, G. et al. Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature 418, 79–85 (2002)
Piper, M. B., Bankier, A. T. & Dear, P. H. A HAPPY map of Cryptosporidium parvum. Genome Res. 8, 1299–1307 (1998)
Konfortov, B. A., Cohen, H. M., Bankier, A. T. & Dear, P. H. A high-resolution HAPPY map of Dictyostelium discoideum chromosome 6. Genome Res. 10, 1737–1742 (2000)
Berriman, M., Aslett, M. & Ivens, A. Parasites are GO. Trends Parasitol. 17, 463–464 (2001)
Florens, L. et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520–526 (2002)
Pachebat, J. A. et al. The 22 kDa component of the protein complex on the surface of Plasmodium falciparum merozoites is derived from a larger precursor, merozoite surface protein 7. Mol. Biochem. Parasitol. 117, 83–89 (2001)
Lasonder, E. et al. Analysis of the Plasmodium falciparum proteome by high accuracy mass spectrometry. Nature 419, 531–542 (2002)
Figueiredo, L. M., Freitas-Junior, L. H., Bottius, E., Olivo-Marin, J. C. & Scherf, A. A central role for Plasmodium falciparum subtelomeric regions in spatial positioning and telomere length regulation. EMBO J. 21, 815–824 (2002)
O'Donnell, R. A. et al. A genetic screen for improved plasmid segregation reveals a role for Rep20 in the interaction of Plasmodium falciparum chromosomes. EMBO J. 21, 1231–1239 (2002)
Katinka, M. D. et al. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414, 450–453 (2001)
Hyman, R., Fung, E. & Dennis, R. W. et al. Sequence of Plasmodium falciparum chromosome 12. Nature 419, 534–536 (2002)
Hapgood, J. P., Riedemann, J. & Scherer, S. D. Regulation of gene expression by GC-rich DNA cis-elements. Cell Biol. Int. 25, 17–31 (2001)
Adhya, S. Multipartite genetic control elements: communication by DNA loop. Annu. Rev. Genet. 23, 227–2250 (1989)
Deitsch, K. W., Calderwood, M. S. & Wellems, T. E. Malaria. Cooperative silencing elements in var genes. Nature 412, 875–876 (2001)
Vazquez-Macias, A. et al. A distinct 5′ flanking var gene region regulates Plasmodium falciparum variant erythrocyte surface antigen expression in placental malaria. Mol. Microbiol. 45, 155–167 (2002)
Quail, M. A. M13 cloning of mung bean nuclease digested PCR fragments as a means of gap closure within A/T-rich, genome sequencing projects. DNA Seq. 12, 355–359 (2001)
Rutherford, K. et al. Artemis: sequence visualization and annotation. Bioinformatics 16, 944–945 (2000)
Salzberg, S. L., Pertea, M., Delcher, A. L., Gardner, M. J. & Tettelin, H. Interpolated Markov models for eukaryotic gene finding. Genomics 59, 24–31 (1999)
Cawley, S. E., Wirth, A. I. & Speed, T. P. Phat—a gene finding program for Plasmodium falciparum. Mol. Biochem. Parasitol. 118, 167–174 (2001)
Zdobnov, E. M. & Apweiler, R. InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847–848 (2001)
Sonnhammer, E. L., von Heijne, G. & Krogh, A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6, 175–182 (1998)
Nielsen, H., Brunak, S. & von Heijne, G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng. 12, 3–9 (1999)
Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nature Genet. 25, 25–29 (2000)
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)
Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 30, 276–280 (2002)
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)
Claros, M. G. & Vincens, P. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241, 779–786 (1996)
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)
Acknowledgements
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.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare that they have no competing financial interests.
Supplementary information
Rights and permissions
About this article
Cite this article
Hall, N., Pain, A., Berriman, M. et al. Sequence of Plasmodium falciparum chromosomes 1, 3–9 and 13. Nature 419, 527–531 (2002). https://doi.org/10.1038/nature01095
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/nature01095
This article is cited by
-
Assessment of genetic diversity of Plasmodium falciparum circumsporozoite protein in Sudan: the RTS,S leading malaria vaccine candidate
Malaria Journal (2021)
-
Genotyping cognate Plasmodium falciparum in humans and mosquitoes to estimate onward transmission of asymptomatic infections
Nature Communications (2021)
-
Characteristic features of the SERA multigene family in the malaria parasite
Parasites & Vectors (2020)
-
Characterization of Plasmodium falciparum NEDD8 and identification of cullins as its substrates
Scientific Reports (2020)
-
Biosynthesis of heme O in intraerythrocytic stages of Plasmodium falciparum and potential inhibitors of this pathway
Scientific Reports (2019)
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.
