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 3D7 genome is undergoing re-annotation.
Published Genome Data
3D7 clone
Responsibility for sequencing the genome was divided on a chromosome by chromsome basis between 3 sequencing centres : The Sanger Institute (U.K.), The Institute for Genomic Research/Naval Medical Research Institute (U.S.A.), and Stanford University.
This work was carried out in collaboration with Chris Newbold of the Molecular Parasitology Group, Institute of Molecular Medicine, Oxford, and Alister Craig of Liverpool School of Tropical Medicine.
IT strain
A project to shotgun sequence the genome of the IT parasite line is underway as a component of the BioMalPar Consortium (European Union 6th Framework Program, Contract number LSHP-LT-2004-503578). This initiative is in collaboration with Chris Newbold of the Molecular Parasitology Group, Institute of Molecular Medicine, Oxford. Image courtesy of D. Ferguson, Oxford. The shotgun reads, assemblies and preliminary annotation are available for download from our ftp site.
Ghanaian Isolate
To facilitate comparative genomic analyses and to circumvent possible artefacts resulting from the study of laboratory cultured strains we have extended our analyses to a clinical isolate obtained from a female patient at St Georges Hospital London. This project is in collaboration with Chris Newbold of the Molecular Parasitology Group, Institute of Molecular Medicine and Sanjeev Krishna at St George's Hospital Medical School. The shotgun reads and preliminary assembly are available from our ftp site.
Studies
- Genome sequencing of Plasmodium species
- Whole genome sequencing of Plasmodium falciparum piggyBac transposon insertional mutants
- RNA-Seq of the blood-stage transcriptome of Plasmodium falciparum IT4 and HB3
- Integrated studies of the development of natural immunity to malaria in children in Kilifi district
- Plasmodium falciparum E5 genome sequencing
- Sequencing of Plasmodium falciparum reference isolates for genotyping
- Genome sequencing of Plasmodium falciparum clones from the progeny of 3D7xHB3 genetic cross
- Whole genome sequencing of Plasmodium falciparum Dd2 clones
- Plasmodium falciparum enrichment tests
- WGS of Plasmodium falciparum 3D7
- WGS of Plasmodium falciparum IT
- Whole genome sequencing of Plasmodium falciparum progeny from HB3-Dd2 cross
Genome sequencing of Plasmodium species
Sample | Strain | Run Accession |
|---|---|---|
| Pf_TM180-NoPCR | TM180 | ERR237543 |
Whole genome sequencing of Plasmodium falciparum piggyBac transposon insertional mutants
RNA-Seq of the blood-stage transcriptome of Plasmodium falciparum IT4 and HB3
Integrated studies of the development of natural immunity to malaria in children in Kilifi district
Sample | Strain | Run Accession |
|---|---|---|
| Pf_12 | Unknown | ERR204288 |
| Pf_7 | Unknown | ERR204287 |
| Pf_9 | Unknown | ERR204286 |
| Pf_4 | Unknown | ERR204281 |
| Pf_6 | Unknown | ERR204280 |
| Pf_2 | Unknown | ERR204279 |
| Pf_5 | Unknown | ERR204278 |
| Pf_1 | Unknown | ERR204277 |
| Pf_11 | Unknown | ERR204285 |
| Pf_10 | Unknown | ERR204284 |
| Pf_8 | Unknown | ERR204283 |
| Pf_3 | Unknown | ERR204282 |
Plasmodium falciparum E5 genome sequencing
Sample | Strain | Run Accession |
|---|---|---|
| 3D7-E5 | E5 | ERR034866 |
Sequencing of Plasmodium falciparum reference isolates for genotyping
Sample | Strain | Run Accession |
|---|---|---|
| 7G8 | 7G8 | ERR019313 |
| EH | Dd2 | ERR019312 |
| EH | Dd2 | ERR019311 |
| BK035m0c1 | Dd2 | ERR019314 |
Genome sequencing of Plasmodium falciparum clones from the progeny of 3D7xHB3 genetic cross
Sample | Strain | Run Accession |
|---|---|---|
| X33 | Unknown | ERR034867 |
| X33 | Unknown | ERR034872 |
| XP8 | Unknown | ERR034868 |
| XP8 | Unknown | ERR034873 |
| X10 | Unknown | ERR034869 |
| X10 | Unknown | ERR034874 |
| X4 | Unknown | ERR034870 |
| X4 | Unknown | ERR034875 |
| XP2 | Unknown | ERR034871 |
| XP2 | Unknown | ERR034876 |
Whole genome sequencing of Plasmodium falciparum Dd2 clones
Sample | Strain | Run Accession |
|---|---|---|
| ParentalDd2_NoPCR | Dd2 | ERR019427 |
| Clone1Dd2_NoPCR | Dd2 | ERR019428 |
| Clone2Dd2_NoPCR | Dd2 | ERR019429 |
| Clone3Dd2_NoPCR | Dd2 | ERR019430 |
Plasmodium falciparum enrichment tests
Sample | Strain | Run Accession |
|---|---|---|
| ech_1 | Unknown | ERR018814 |
WGS of Plasmodium falciparum 3D7
Sample | Strain | Run Accession |
|---|---|---|
| 3D7-700L | 3D7 | ERR019077 |
| 3D7-3000L | 3D7 | ERR019076 |
| 3D7_500_NoPCR_GAII | 3D7 | ERR034295 |
| 3D7_500_NoPCR_GAII | 3D7 | ERR036168 |
| Pf3D7_454 | 3D7 | ERR163029 |
| Pf3D7_SOLiD5500 | 3D7 | ERR163028 |
| Pf3D7_Sanger | 3D7 | ERR163027 |
WGS of Plasmodium falciparum IT
-
Genome sequence of the human malaria parasite Plasmodium falciparum.
Nature 2002;419;6906;498-511
PUBMED: 12368864; DOI: 10.1038/nature01097
-
Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.
Nature 2002;419;6906;527-31
PUBMED: 12368867; DOI: 10.1038/nature01095
-
The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum.
Nature 1999;400;6744;532-8
PUBMED: 10448855; DOI: 10.1038/22964

