Plasmodium falciparum is the most deadly of the five Plasmodium species that cause human malaria. Malaria has a massive impact on human health; it is the worlds second biggest killer after tuberculosis. Around 300 million clinical cases occur each year resulting in between 1.5 - 2.7 million deaths annually, the majority in sub-saharan Africa. It is estimated that 3,000 children under the age of five years fall victim to malaria each day. Around 40% of the worlds population are at risk.
The P. falciparum 3D7 nuclear genome is 23.3 Mb in size, with a karyotype of 14 chromosomes. The G+C content is approximately 19%. The P. falciparum genome is undergoing re-annotation. This process started in October 2007 with a weeklong workshop co-organized by staff from the Wellcome Trust Sanger Intistute and the EuPathDB team. Ongoing curation and sequence checking is being carried out by the Pathogen Genomics group.
The most recent sequence updates and annotations for the P. falciparum 3D7 genome can be found in GeneDB.
GeneDB has been funded by Wellcome Trust to provide full curation support for P. falciparum 3D7 to meet the needs of the community. New annotations are constantly being added to keep up with published manuscripts and feedback from the Plasmodium research community. In collaboration with EuPathDB, genomic sequence data and annotations are regularly deposited on PlasmoDB where they can be integrated with other datasets and queried using customized queries.
A high quality draft genome of Plasmodium falciparum 3D7 was produced by an international consortium in 2002 (Gardner et al., Nature 2002; 419:498-511).
However, the completed genome, with no gaps, is being finished at the Sanger Institute. The latest version (v3.0) comprises systematically corrected and reassembled sequence, plus genome-wide re-annotation, incorporating annotations from a community annotation workshop, ongoing community feedback and detailed manual inspection by curation staff at the Sanger Institute. A manuscript describing the latest version is in preparation. We therefore request that you consult with the Principle Investigators before undertaking large scale analyses of the annotation or underlying sequence.
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P. falciparum 3D7 apicoplast now on GeneDB
The complete P. falciparum 3D7 apicoplast has now been included on GeneDB resulting in genome version 3.1 (August 2015). In the original genome project that was published in 2002 the P. falciparum 3D7 apicoplast was not sequenced. For the re-annotation process the apicoplast from P. falciparum strain C10 was temporarily used (PFC10_IRAB) and included in the genome version 2.1.4. The new apicoplast has a length of 34 kb and consists of one contig.
New version of the genome
A new version of the P. falciparum 3D7 genome is now available (September 2011). This sequence version is an upgrade from version 2.1.4 to version 3. Differences include the correction of major mis-assemblies on chromosome 7 and 8, the replacement of all “N”s in the genome with the correct sequence and the correction of hundreds of sequencing errors. In order to comply to embl standards we decided to make the confusing old-style systematic identifiers less prominent and assign new identifiers to all protein-coding and non-protein coding genes. All previous identifiers are retained as searchable synonyms. A conversion list of new identifiers to old identifiers can be downloaded from the ftp site.