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Plasmodium falciparum Arrives in GenBank
The recently completed genome of the malaria parasite Plasmodium falciparum is available in GenBank and displayed in the Entrez Map Viewer. As reported in the October 3rd, 2002 issue of Nature (search in PubMed for PMID 12368864), P. falciparum clone 3D7 consists of a 23-megabase nuclear genome of 14 chromosomes assembled from finished high-throughput genomic sequence (HTGS, Phase 3). The genome was sequenced by members of the Malaria Genome Sequencing Consortium including The Institute for Genomic Research (TIGR), in collaboration with the US Naval Medical Research Center, the Sanger Institute, and the Stanford Genome Technology Center at Stanford University.
| Click on figure to view enlarged version |
Figure 1: Entrez Map Viewer display of BLAST hit to chromosome 9 of P. falciparum for unknown Arabidopsis protein BAB01718. The BLAST hit coincides with P. falciparum protein NP_704698, as seen on the Gene map, and predicted protein EAA19956 from P. yoelii, as seen on the “Py prot” map.
The sequence of each P. falciparum chromosome is represented in the Entrez Genomes database as a separate RefSeq record (with accession number of the form NC_XXXXXX ) and may be found by the query “Plasmodium falciparum 3D7[organism]” in the Entrez Genomes.
The Entrez document summary for the sequence of chromosome 9, returned by the above query, appears as follows:
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The accession number in the document summary is a link to a Map Viewer display of the assembled sequence data, gene annotations, and genetic linkages.
Sequence maps available in the Map Viewer for P. falciparum include Chromosome, Component, and Gene maps. The chromosome sequence map shows the genomic sequence assembled from smaller components, visible on the components map. The genes sequence map displays genes that have been annotated on the chromosome including known and putative genes placed using blastx alignments of reference sequence proteins to the chromosome sequence. Another informative map is the “Py Protein” map, which presents reciprocal best hits between predicted proteins encoded in the P. falciparum genome and those predicted to be encoded in the whole genome shotgun (WGS) sequences of P. yoelii, a rodent malaria parasite. The order of the hits shown on the “Py protein” map reflects the order of the corresponding genes on the P. falciparum “gene_seq” map.
A Genome BLAST against the P. falciparum genome using unidentified A. thaliana protein BAB01718 leads to the genome view shown in the figure above. Note the hit to the P. falciparum genome in an area encoding a protein that is a reciprocal best hit to a P. yoelii protein.
A variety of Plasmodium data has been incorporated into a malaria-related resource called Malaria Triad: Genetics & Genomics that is available from NCBI at:
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The site combines information on the organisms involved in malaria research and provides access to services for data retrieval, genetic and genomic analysis of the sequence data, and malaria-related news. The Plasmodium genomes data (P. falciparum, P. yoelii and P. vivax), as well the genome of Anopheles gambiae, can be accessed from the malaria page along with the results of pre-computed sequence and literature searches. BLAST services have been tailored to search against malaria-related organisms and the Plasmodium falciparum and Plasmodium yoelii genomes have been incorporated into Genome BLAST (see figure 1), in which BLAST results are displayed in their genomic context using the Entrez Map Viewer.
The P. falciparum genome can be downloaded from the NCBI FTP site at:
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