Plasmodium falciparum

Plasmodium falciparum is the deadliest of five human malaria species and responsible for the majority of malaria related deaths. There are around 300 million clinical cases occur each year resulting in at least one million deaths annually, predominantly in sub-saharan Africa. An estimated 3,000 children, under the age of five, fall victim to malaria each day and around 40% of the worlds population are at risk of infection.

Data Downloads

[Genome Research Limited]

The canonical reference P. falciparum clone 3D7 was first published by Gardner et al. in 2002. The nuclear genome was described as 22.9 Mb and essentially complete, with 14 chromosomes, a G+C content of approximately 19%, 5268 genes and approximately 80 gaps.

Genome improvement of P. falciparum 3D7

Since publication efforts have continued to improve both the sequence and annotation. The latest annotation is continually updated in GeneDB and used to periodically update PlasmoDB. A complete telomere-to-telomere sequence is in preparation that includes full assessment of accuracy using REAPR (Hunt et al). The current version (v3.0) has 5369 genes, some re-assembled regions of chromosomes 7, 8 and 13, comprehensive reannotation and no gaps. A publication describing the complete methodology and important changes is in preparation. Please refer to Data Use Statement.

Genome improvement of P. falciparum 3D7

Since publication efforts have continued to improve both the sequence and annotation. The latest annotation is continually updated in GeneDB and used to periodically update PlasmoDB. A complete telomere-to-telomere sequence is in preparation that includes full assessment of accuracy using REAPR (Hunt et al). The current version (v3.0) has 5369 genes, some re-assembled regions of chromosomes 7, 8 and 13, comprehensive reannotation and no gaps. A publication describing the complete methodology and important changes is in preparation. Please refer to Data Use Statement.

Other P. falciparum sequencing projects

A draft sequence of P. falciparum IT clone was produced using Sanger sequencing (funded as a component of the BioMalPar Consortium, European Union 6th Framework Program, Contract number LSHP-LT-2004-503578) and more recently using Illumina Sequence-by-Synthesis. An annotation of the latest version can be accessed at GeneDB and is currently unpublished. Please refer to Data Use Statement.

Large-scale resequencing of global P. falciparum isolates is being undertaken as part of the Malaria Programme.

Whole genome sequencing of Plasmodium falciparum piggyBac transposon insertional mutants

Sample

Strain

Run Accession

PB-39UnknownERR224767
PB-116UnknownERR224768
PB-119UnknownERR224769
PB-59UnknownERR224770
PB-13UnknownERR224771
PB-46UnknownERR224772
PB-48UnknownERR224773
PB-43UnknownERR224774
PB-49UnknownERR224775
PB-94UnknownERR224776
E5-Not1UnknownERR224777
NF54-mCherryUnknownERR224778
PB-69UnknownERR224779
PB-47UnknownERR224780
PB-3UnknownERR224781
PB-27UnknownERR224782
PB-79UnknownERR224783
PB-23UnknownERR224784
PB-8UnknownERR224785
PB-19UnknownERR224786
PB-32UnknownERR224787
IGM2F11UnknownERR224788
IGM2H3UnknownERR224789
IGM2E2UnknownERR224790
F3_CAF1UnknownERR224766
C9_PF13_0027UnknownERR224765
06092208UnknownERR224764
NF54UnknownERR224763
HB2UnknownERR224802
F12UnknownERR224801
IGM2F6UnknownERR224800
IGM2A9UnknownERR224799
IGM2H8UnknownERR224798
IGM2G10UnknownERR224797
IGM2G6UnknownERR224796
IGM2H12UnknownERR224795
IGM2E4UnknownERR224794
IGM2G3UnknownERR224793
IGM2D4UnknownERR224792
IGM2B4UnknownERR224791
IGM2D3UnknownERR224814
IGM1C5UnknownERR224813
IGM1B5UnknownERR224812
IGM1A2UnknownERR224811
PB-26UnknownERR224810
PB-29UnknownERR224809
PB-21UnknownERR224808
PB-30UnknownERR224807
PB-44UnknownERR224806
PB-34UnknownERR224805
PB-33UnknownERR224804
PB-14UnknownERR224803
5-Chris-C9NF54-PiggyBac MutantERR224877
5-KnMP_2NF54-PiggyBac MutantERR224876
5-PB-43NF54-PiggyBac MutantERR224875
3-Chris-C9NF54-PiggyBac MutantERR224873
3-KnMP_2NF54-PiggyBac MutantERR224872
3-PB-43NF54-PiggyBac MutantERR224871
5-NF-54_WTNF54 Wild TypeERR224870
5-Phaedra-E5NF54-PiggyBac MutantERR224869
5-KnMP_1NF54-PiggyBac MutantERR224868
5-PB-33NF54-PiggyBac MutantERR224867
3-Phaedra-E5NF54-PiggyBac MutantERR224865
3-KnMP_1NF54-PiggyBac MutantERR224864
3-PB-33NF54-PiggyBac MutantERR224863
5-Shulin-H7NF54-PiggyBac MutantERR224862
5-UknMP4-2012NF54-PiggyBac MutantERR224861
5-PB-27_PB-3NF54-PiggyBac MutantERR224860
5-PB-32NF54-PiggyBac MutantERR224859
3-Shulin-H7NF54-PiggyBac MutantERR224858
3-UknMP4-2012NF54-PiggyBac MutantERR224857
3-PB-27_PB-3NF54-PiggyBac MutantERR224856
3-PB-32NF54-PiggyBac MutantERR224855
5-Shulin-G4NF54-PiggyBac MutantERR224854
5-UknMP3-2012NF54-PiggyBac MutantERR224853
5-PB-69_PB-3NF54-PiggyBac MutantERR224852
5-PB-13NF54-PiggyBac MutantERR224851
3-Shulin-G4NF54-PiggyBac MutantERR224850
3-UknMP3-2012NF54-PiggyBac MutantERR224849
3-PB-69_PB-3NF54-PiggyBac MutantERR224848
3-PB-13NF54-PiggyBac MutantERR224847
5-Rajeev-2NF54-PiggyBac MutantERR224846
5-UknMP2-2012NF54-PiggyBac MutantERR224845
5-PB-29_PB-3NF54-PiggyBac MutantERR224844
5-PB-59NF54-PiggyBac MutantERR224843
3-Rajeev-2NF54-PiggyBac MutantERR224842
3-UknMP2-2012NF54-PiggyBac MutantERR224841
3-PB-29_PB-3NF54-PiggyBac MutantERR224840
3-PB-59NF54-PiggyBac MutantERR224839
5-Rajeev-1NF54-PiggyBac MutantERR224838
5-UknMP1-2012NF54-PiggyBac MutantERR224837
5-PB-47_PB-3NF54-PiggyBac MutantERR224836
5-PB-119NF54-PiggyBac MutantERR224835
3-Rajeev-1NF54-PiggyBac MutantERR224834
3-UknMP1-2012NF54-PiggyBac MutantERR224833
3-PB-47_PB-3NF54-PiggyBac MutantERR224832
3-PB-119NF54-PiggyBac MutantERR224831
5-Chris-E8NF54-PiggyBac MutantERR224830
5-KnMP_6NF54-PiggyBac MutantERR224829
5-PB-3NF54-PiggyBac MutantERR224828
5-PB-116NF54-PiggyBac MutantERR224827
3-Chris-E8NF54-PiggyBac MutantERR224826
3-KnMP_6NF54-PiggyBac MutantERR224825
3-PB-3NF54-PiggyBac MutantERR224824
3-PB-116NF54-PiggyBac MutantERR224823
5-Chris-E3NF54-PiggyBac MutantERR224822
5-KnMP_3NF54-PiggyBac MutantERR224821
5-PB-49NF54-PiggyBac MutantERR224820
5-PB-39NF54-PiggyBac MutantERR224819
3-KnMP_3NF54-PiggyBac MutantERR224817
3-PB-49NF54-PiggyBac MutantERR224816
3-PB-39NF54-PiggyBac MutantERR224815
NF54_NoPCRNF54ERR223481
NF54_NoPCRNF54ERR268105
HB2_1UnknownERR338888
HB3_1UnknownERR337902

Plasmodium falciparum enrichment tests

Sample

Strain

Run Accession

ech_1UnknownERR018814

Genome-Wide Subnuclear Architecture in Antigenically Selected Lines of P.falciparum

Sample

Strain

Run Accession

3C_HindIIIITERR333727
3C_MboIITERR333728
HiC_HindIIIITERR333729
HiC_MboIITERR333730
3C_H_OFF_DCJUnknownERR333740
HiC_M_ON_DCJUnknownERR333731
3C_H_B15C2UnknownERR333741
HiC_M_Dd2UnknownERR333732
3C_H_Rev1UnknownERR333742
HiC_M_PQP1UnknownERR333733
3C_H_3D7UnknownERR333743
3C_E_ER3D7UnknownERR333744
HiC_H_ER3D7UnknownERR333734
HiCM_E_LT3D7UnknownERR333745
3C_H_LT3D7UnknownERR333746
HiC_M_OFF_DCJUnknownERR333735
3C__H_ON_DCJUnknownERR333747
HiC_H_B15C2UnknownERR333736
3C_M_Dd2UnknownERR333748
HiC_H_Rev1UnknownERR333737
3C_M_PQP1UnknownERR333749
HiC_H_3D7UnknownERR333738
HiCM_E_ER3D7UnknownERR333750
3C_H_ER3D7UnknownERR333751
HiC_M_LT3D7UnknownERR333739
3C_M_OFF_DCJUnknownERR333761
HiC_H_ON_DCJUnknownERR333752
3C_M_B15C2UnknownERR333762
HiC_H_Dd2UnknownERR333753
3C_M_Rev1UnknownERR333763
HiC_H_PQP1UnknownERR333754
3C_M_3D7UnknownERR333764
3C_M_ER3D7UnknownERR333765
HiCM_H_ER3D7UnknownERR333766
3C_M_LT3D7UnknownERR333767
HiC_H_OFF_DCJUnknownERR333755
3C_M_ON_DCJUnknownERR333768
HIC_M_B15C2UnknownERR333756
3C_H_Dd2UnknownERR333769
HiC_M_Rev1UnknownERR333757
3C_H_PQP1UnknownERR333770
HiC_M_3D7UnknownERR333758
HiC_M_ER3D7UnknownERR333759
3C_E_LT3D7UnknownERR333771
HiC_H_LT3D7UnknownERR333760
HiCM_H_LT3D7UnknownERR333772
A4posH3_3CITERR333773
A4negH3_3CITERR333774
3G8H3_3C_1ITERR333775
A4posMbo3C_1ITERR333776
A4negMbo3C_1ITERR333777
3G8Mbo3C_1ITERR333778
A4posH3ligITERR333779
3G8H3LigITERR333780
A4unselH3LigITERR333781
A4posMboLigITERR333782
3G8MboLigITERR333783
A4unselMboLigITERR333784
A4posH3HiCITERR333785
A4negH3HiCITERR333786
3G8H3HiCITERR333787
A4posMboHiCITERR333788
A4negMboHiCITERR333789
3G8MboHiCITERR333790
  • Genome sequence of the human malaria parasite Plasmodium falciparum.

    Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM and Barrell B

    Nature 2002;419;6906;498-511

  • Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.

    Hall N, Pain A, Berriman M, Churcher C, Harris B, Harris D, Mungall K, Bowman S, Atkin R, Baker S, Barron A, Brooks K, Buckee CO, Burrows C, Cherevach I, Chillingworth C, Chillingworth T, Christodoulou Z, Clark L, Clark R, Corton C, Cronin A, Davies R, Davis P, Dear P, Dearden F, Doggett J, Feltwell T, Goble A, Goodhead I, Gwilliam R, Hamlin N, Hance Z, Harper D, Hauser H, Hornsby T, Holroyd S, Horrocks P, Humphray S, Jagels K, James KD, Johnson D, Kerhornou A, Knights A, Konfortov B, Kyes S, Larke N, Lawson D, Lennard N, Line A, Maddison M, McLean J, Mooney P, Moule S, Murphy L, Oliver K, Ormond D, Price C, Quail MA, Rabbinowitsch E, Rajandream MA, Rutter S, Rutherford KM, Sanders M, Simmonds M, Seeger K, Sharp S, Smith R, Squares R, Squares S, Stevens K, Taylor K, Tivey A, Unwin L, Whitehead S, Woodward J, Sulston JE, Craig A, Newbold C and Barrell BG

    Nature 2002;419;6906;527-31

  • The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum.

    Bowman S, Lawson D, Basham D, Brown D, Chillingworth T, Churcher CM, Craig A, Davies RM, Devlin K, Feltwell T, Gentles S, Gwilliam R, Hamlin N, Harris D, Holroyd S, Hornsby T, Horrocks P, Jagels K, Jassal B, Kyes S, McLean J, Moule S, Mungall K, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutter S, Skelton J, Squares R, Squares S, Sulston JE, Whitehead S, Woodward JR, Newbold C and Barrell BG

    Nature 1999;400;6744;532-8

Data Use Statement

This sequencing centre plans on publishing the completed and annotated sequences in a peer-reviewed journal as soon as possible. Permission of the principal investigator should be obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or genome scale. See our data sharing policy.

Sequencing enquiries

Please address all sequencing enquiries to: pathinfo@sanger.ac.uk

* quick link - http://q.sanger.ac.uk/2zec5047