Genome sequence of the human malaria parasite Plasmodium falciparum
Open accessAbstract
The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria.
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1 μg of P. falciparum DNA is equal to 4.067 × 107 genome copies, or one genome copy in 24.6 fg of DNA.
“we calculated that 1 μg of P. falciparum DNA is equal to 4.067 × 107 genome copies or one genome copy in 24.6 fg of DNA.”
From Real-Time PCR for Detection and Identification of <i>Plasmodium</i> spp (2005) · cites this paper as [11]
The Genome structure and content section reports that the P. falciparum 3D7 nuclear genome is 22.8 Mb, providing the genome size on which the citing authors could base their calculation. Our copy does not report 24.6 fg per genome or 4.067 × 10⁷ genome copies per μg; the citing sentence identifies those figures as its own calculation. (LLM, conf=0.82)
Experimental — accuracy not yet measuredThe 18S rRNA gene contains both highly conserved and variable regions, and at least five copies of the gene are dispersed on separate chromosomes of the Plasmodium genome.
“The 18S rRNA gene was chosen as the target since it contains both highly conserved and variable regions, and at least five copies of the gene are dispersed on separate chromosomes of the Plasmodium genome (11, 20).”
From Real-Time PCR for Detection and Identification of <i>Plasmodium</i> spp (2005) · cites this paper as [11]
The Genome structure and content section identifies 18S-containing rRNA units on chromosomes 1, 5, 7, 11 and 13, supporting at least five copies on separate chromosomes. It says sequences differ between rRNA units, but does not establish that the 18S gene itself contains both highly conserved and variable regions. No page number is available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredTargeting a gene with multiple copies dispersed throughout the Plasmodium genome increases the sensitivity of the assay compared to targeting a single-copy gene.
“By targeting a gene with multiple copies dispersed throughout the Plasmodium genome (11), the sensitivity of this assay is greater than if a single-copy gene was chosen.”
From Real-Time PCR for Detection and Identification of <i>Plasmodium</i> spp (2005) · cites this paper as [11]
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Plasmodium—a brief introduction to the parasites causing human malaria and their basic biology
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“However, as the genomic information encoded in the nuclear genome of the parasites became available [110], it gradually became evident that the Plasmodium apicoplast is involved in plant-type metabolic pathways including isoprenoid biosynthesis [111], type II fatty acid biosynthesis [112] and haem biosynthesis [113].”
BackgroundYeast Model Uncovers Dual Roles of Mitochondria in the Action of Artemisinin
Li, W., Mo, W., Shen, D., Sun, L., Wang, J., Lu, S., Gitschier, J. M., & Zhou, B. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010036 · Cited by 304 · see citing works
del Prete, S., Vullo, D., Fisher, G., Andrews, K., Poulsen, S., Capasso, C., & Supuran, C. (2014) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2014.08.015 · Cited by 312 · see citing works
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
Kapusta, A., & Feschotte, C. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.08.004 · Cited by 291 · see citing works
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“falciparum proteins (17) are targets of protective antibodies, the precise mechanisms by which these antibodies protect, and why they are only acquired after years of repeated infections— all critically important questions for blood-stage malaria vaccine development, an effort that so far has been largely empiric and…”
BackgroundDesigning the next generation of medicines for malaria control and eradication
Burrows, J. N., van Huijsduijnen, R. H., Möhrle, J. J., Oeuvray, C., & Wells, T. N. C. (2013) · Malaria Journal · doi:10.1186/1475-2875-12-187 · Cited by 282 · see citing works
“With the sequencing of the parasite genomes [3-5], new potential drug targets have emerged.”
BackgroundOn the Cytoadhesion of <i>Plasmodium vivax</i> –Infected Erythrocytes
Carvalho, B. O., Lopes, S. C. P., Nogueira, P. A., Orlandi, P. P., Bargieri, D. Y., Blanco, Y. C., Mamoni, R., Leite, J. A., Rodrigues, M. M., Soares, I. S., et al. (2010) · The Journal of Infectious Diseases · doi:10.1086/654815 · Cited by 299 · see citing works
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The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum
Neafsey, D., Galinsky, K., Jiang, R. H. Y., Young, L., Sykes, S., Saif, S., Gujja, S., Goldberg, J., Young, S. K., Zeng, Q., et al. (2012) · Nature Genetics · doi:10.1038/ng.2373 · Cited by 286 · see citing works
Self-citationReal-Time PCR for Detection and Identification of <i>Plasmodium</i> spp
Mangold, K. A., Manson, R. U., Koay, E. S. C., Stephens, L., Regner, M., Thomson, R. B., Peterson, L. R., & Kaul, K. L. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.5.2435-2440.2005 · Cited by 278 · see citing works
Application of next-generation sequencing technologies in virology
Radford, A. D., Chapman, D., Dixon, L. K., Chantrey, J., Darby, A. C., & Hall, N. (2012) · Journal of General Virology · doi:10.1099/vir.0.043182-0 · Cited by 290 · see citing works
“…first-generation sequencing technology on a large scale in highly specialized sequencing centres, the first large highprofile genomes were published, notably those for Homo sapiens, Plasmodium falciparum and Mycobacterium tuberculosis (Cole et al., 1998; Gardner et al., 2002; Lander et al., 2001).”
BackgroundSelf-citationKemen, E. M., Gardiner, A., Schultz‐Larsen, T., Kemen, A. C., Balmuth, A. L., Robert‐Seilaniantz, A., Bailey, K., Holub, E. B., Studholme, D. J., MacLean, D., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001094 · Cited by 256 · see citing works
Innate Immune Recognition of an AT-Rich Stem-Loop DNA Motif in the Plasmodium falciparum Genome
Sharma, S., DeOliveira, R. B., Kalantari, P., Parroche, P., Goutagny, N., Jiang, Z., Chan, J., Bartholomeu, D. C., Lauw, F. N., Hall, J. P., et al. (2011) · Immunity · doi:10.1016/j.immuni.2011.05.016 · Cited by 258 · see citing works
Lorenzi, H., Khan, A., Behnke, M., Namasivayam, S., Swapna, L. S., Hadjithomas, M., Karamycheva, S., Pinney, D. F., Brunk, B., Ajioka, J., et al. (2016) · Nature Communications · doi:10.1038/ncomms10147 · Cited by 266 · see citing works
“Examples include: the expansion of surface antigen variants encoded by VAR genes in the Plasmodium falciparum genome 50 , and the unrelated yet expanded VIR genes in Plasmodium vivax 51 , variant surface glycoprotein encoding genes ( VSG ) in Trypanosoma brucei 52 , and the expansion of RXLR…”
Self-citationSimulation-based comprehensive benchmarking of RNA-seq aligners
Baruzzo, G., Hayer, K. E., Kim, E. J., Camillo, B. D., FitzGerald, G., & Grant, G. (2016) · Nature Methods · doi:10.1038/nmeth.4106 · Cited by 261 · see citing works
“The P. falciparum genome was used because it is notorious for being difficult, mainly because it is approximately 80% AT rich in exons and 90% in introns and intergenic regions 20 .”
MethodChuma, I., Isobe, C., Hotta, Y., Ibaragi, K., Futamata, N., Kusaba, M., Yoshida, K., Terauchi, R., Fujita, Y., Nakayashiki, H., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002147 · Cited by 260
“falciparum, genes involved in antigenic variation (var, rif, etc) are concentrated in subtelomeric chromosomal regions [43].”
BackgroundIsmail, H. M., Barton, V., Phanchana, M., Charoensutthivarakul, S., Wong, M. H. L., Hemingway, J., Biagini, G. A., O’Neill, P. M., & Ward, S. A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600459113 · Cited by 261 · see citing works
Generating high quality libraries for DIA MS with empirically corrected peptide predictions
Searle, B. C., Swearingen, K. E., Barnes, C. A., Schmidt, T., Gessulat, S., Küster, B., & Wilhelm, M. (2020) · Nature Communications · doi:10.1038/s41467-020-15346-1 · Cited by 251 · see citing works
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“Other than the genome statistics for Oxytricha trifallax, which were determined in this study, table statistics were obtained from the following sources: a - [2], b - [22,116], c - [117], d - [99], e - [94], f - [56] (the number of chromosomes is an estimate), g -[118], h - [119], i - [120], - [64] (for a single stage…”
MethodIndels, structural variation, and recombination drive genomic diversity in Plasmodium falciparumPreprint
Miles, A., Iqbal, Z., Vauterin, P., Pearson, R. D., Campino, S. G., Theron, M., Gould, K., Mead, D. G., Drury, E., O’Brien, J., et al. (2016) · Genome Research · doi:10.1101/gr.203711.115 · Cited by 234 · see citing works
“The highly compact 23-Mbp genome has an extremely biased nucleotide composition, with 80.6% (A + T) content overall and ∼ 90% (A + T) in noncoding regions (Gardner et al. 2002).”
Influential21st Century Natural Product Research and Drug Development and Traditional Medicines
Ngo, L., Okogun, J., & Folk, W. (2013) · Natural product reports (Print) · doi:10.1039/c3np20120a · Cited by 229 · see citing works
Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
Girgis, H. Z. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0654-5 · Cited by 228 · see citing works
“6% [47].”
Bopp, S. E. R., Manary, M. J., Bright, A. T., Johnston, G. L., Dharia, N. V., Luna, F. L., McCormack, S., Plouffe, D., McNamara, C. W., Walker, J. R., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003293 · Cited by 221 · see citing works
“Walliker) [49,50] and was used in the genome-sequencing project [51].”
MethodCollins, C. R., Das, S., Wong, E., Andenmatten, N., Stallmach, R., Hackett, F., Herman, J.-P., Müller, S., Meissner, M., & Blackman, M. (2013) · Molecular Microbiology · doi:10.1111/mmi.12206 · Cited by 227
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Sexual development in Plasmodium parasites: knowing when it's time to commit
Josling, G., & Llinás, M. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3519 · Cited by 223 · see citing works
Claessens, A., Hamilton, W. L., Kekre, M., Otto, T. D., Faizullabhoy, A., Rayner, J. C., & Kwiatkowski, D. P. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004812 · Cited by 210 · see citing works
“3610 bp [42].”
Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies
Muellenbeck, M. F., Ueberheide, B. M., Amulic, B., Epp, A., Fenyö, D., Busse, C. E., Esen, M., Theisen, M., Mordmüller, B. G., & Wardemann, H. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20121970 · Cited by 199 · see citing works
“Protective immunity to control clinical disease caused by parasite growth in red blood cells (RBCs) takes years to develop and requires repeated infections (Garnham, 1949).”
BackgroundThe structural basis for CD36 binding by the malaria parasite
Hsieh, F.-L., Turner, L., Bolla, J. R., Robinson, C. V., Lavstsen, T., & Higgins, M. K. (2016) · Nature Communications · doi:10.1038/ncomms12837 · Cited by 235 · see citing works
Malaria's deadly grip: cytoadhesion of Plasmodium falciparum -infected erythrocytes
Smith, J. D., Rowe, J. A., Higgins, M. K., & Lavstsen, T. (2013) · Cellular Microbiology · doi:10.1111/cmi.12183 · Cited by 225 · see citing works
“Some rosetting variants also bind the Fc region of human IgM (Ghumra et al., 2008), a process that strengthens rosetting interactions (Scholander et al., 1996).”
Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum
Caro, F., Miller, M., & Derisi, J. (2012) · Malaria Journal · doi:10.1186/1475-2875-11-22 · Cited by 213
Isoprenoid biosynthesis in eukaryotic phototrophs: A spotlight on algae
Lohr, M., Schwender, J., & Polle, J. E. W. (2011) · Plant Science · doi:10.1016/j.plantsci.2011.07.018 · Cited by 244 · see citing works
Lee, R. A., de Puig, H., Nguyen, P. Q., Angenent-Mari, N. M., Donghia, N. M., McGee, J. P., Dvorin, J. D., Klapperich, C. M., Pollock, N. R., & Collins, J. J. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2010196117 · Cited by 244 · see citing works
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“The methanol extract has exhibited significant antiplasmodial effects against malaria parasite, Plasmodium yoelii nigeriensis.”
BackgroundInfluentialVariant surface antigens of Plasmodium falciparum and their roles in severe malaria
Wahlgren, M., Goel, S., & Akhouri, R. R. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.47 · Cited by 237 · see citing works
Avril, M., Tripathi, A. K., Brazier, A. J., Andisi, C., Janes, J. H., Soma, V. L., Sullivan, D. J., Bull, P. C., Stins, M. F., & Smith, J. D. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120534109 · Cited by 185 · see citing works
Armstrong, J. F., Faccenda, E., Harding, S. D., Pawson, A. J., Southan, C., Sharman, J. L., Campo, B., Cavanagh, D. R., Alexander, S. P. H., Davenport, A. P., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz951 · Cited by 186 · see citing works
The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum
King, R., Urban, M., Hammond-Kosack, M. C. U., Hassani‐Pak, K., & Hammond-Kosack, K. E. (2015) · BMC Genomics · doi:10.1186/s12864-015-1756-1 · Cited by 228 · see citing works
“Telomeres are established in many species as sites of high Single Nucleotide Polymorphism (SNP) frequency and structural rearrangement [52–54].”
BackgroundPease, B. N., Huttlin, E. L., Jedrychowski, M. P., Talevich, E., Harmon, J., Dillman, T., Kannan, N., Doerig, C., Chakrabarti, R., Gygi, S., et al. (2013) · Journal of Proteome Research · doi:10.1021/pr400394g · Cited by 187 · see citing works
Progress with Plasmodium falciparum sporozoite (PfSPZ)-based malaria vaccines
Richie, T., Billingsley, P., Sim, B. K., James, E., Chakravarty, S., Epstein, J., Lyke, K., Mordmüller, B., Alonso, P., Duffy, P., et al. (2015) · Vaccine · doi:10.1016/j.vaccine.2015.09.096 · Cited by 183
Self-citationKalantari, P., DeOliveira, R. B., Chan, J., Corbett, Y., Rathinam, V. A. K., Stutz, A., Latz, E., Gazzinelli, R. T., Golenbock, D. T., & Fitzgerald, K. A. (2014) · Cell Reports · doi:10.1016/j.celrep.2013.12.014 · Cited by 198 · see citing works
Dziekan, J. M., Yu, H., Chen, D., Dai, L., Wirjanata, G., Larsson, A., Prabhu, N., Sobota, R. M., Bozdech, Z., & Nordlund, P. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aau3174 · Cited by 220 · see citing works
Protein complex directs hemoglobin-to-hemozoin formation in Plasmodium falciparum
Chugh, M., Sundararaman, V., Kumar, S., Reddy, V. S., Siddiqui, W., Stuart, K., & Malhotra, P. (2013) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1218412110 · Cited by 180 · see citing works
“Although our understanding of parasite biology has advanced considerably with the sequencing of the Plasmodium genome (15), no new class of antimalarials has been introduced into clinical practice since 1996.”
BackgroundPlasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution
Rutledge, G. G., Böhme, U., Sanders, M. J., Reid, A. J., Cotton, J. A., Maïga‐Ascofaré, O., DJIMDÉ, A. A., Apinjoh, T. O., Amenga-Etego, L. N.-K., Manske, M., et al. (2017) · Nature · doi:10.1038/nature21038 · Cited by 190 · see citing works
Self-citationNiang, M., Bei, A., Madnani, K., Pelly, S., Dankwa, S., Kanjee, U., Gunalan, K., Amaladoss, A., Yeo, K. P., Bob, N. S., et al. (2014) · Cell Host and Microbe · doi:10.1016/j.chom.2014.06.004 · Cited by 178
“Analysis of the P. falciparum genome (Gardner et al., 2002) has identified three major families of variant genes: the var genes encoding Erythrocyte Membrane Protein 1 (PfEMP1); the repetitive inter- C spersed family (rif); and the subtelomeric variant open reading frame (stevor) genes encoding the…”
BackgroundGenetic Investigation of Tricarboxylic Acid Metabolism During the Plasmodium falciparum Lifecycle
Ke, H.-J., Lewis, I., Morrisey, J. M., McLean, K., Ganesan, S. M., Painter, H. J., Mather, M., Jacobs-Lorena, M., Llinás, M., & Vaidya, A. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.03.011 · Cited by 176 · see citing works
“Normalized intensities were extracted using Agilent Feature Extractor Software Version 9.5 by the standard protocol and uploaded to the Princeton University Microarray Database (PUMA.princeton.edu) for analysis.”
InfluentialSelf-citationA comprehensive evaluation of assembly scaffolding tools
Hunt, M., Newbold, C., Berriman, M., & Otto, T. D. (2014) · Genome biology · doi:10.1186/gb-2014-15-3-r42 · Cited by 174 · see citing works
“These comprised Illumina reads from the Staphylococcus aureus , Rhodobacter sphaeroides , the human chromosome 14 GAGE datasets and the Plasmodium falciparum clone 3D7 reference genome [21].”
Self-citationChan, J.-A., Fowkes, F. J. I., & Beeson, J. G. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1614-3 · Cited by 167 · see citing works
“The var genes can be classified into three main subgroups based on their upstream promoter regions (upsA, upsB and upsC) and the single-copy conserved intergenomic genes var1 and var2csa [142–145].”
Background(2015) · Advances in Parasitology · doi:10.1016/bs.apar.2015.02.004 · Cited by 162 · see citing works
ITS1: a DNA barcode better than ITS2 in eukaryotes?
Wang, X., Liu, C., Huang, L., Bengtsson-Palme, J., Chen, H.-M., Zhang, J.-H., Cai, D., & Li, J.-Q. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12325 · Cited by 173
“The lowest GC content in the genomes of some species has been reported to be close to 20% (Gardner et al. 2002; Hu et al. 2007), and thus, the GC content cutoffs were set at 20% and 80%.”
BackgroundMcKie, S. J., Neuman, K. C., & Maxwell, A. (2021) · BioEssays · doi:10.1002/bies.202000286 · Cited by 205 · see citing works
Malaria parasite DNA-harbouring vesicles activate cytosolic immune sensors
Sisquella, X., Ofir‐Birin, Y., Pimentel, M. A., Cheng, L., Karam, P. A., Sampaio, N. G., Penington, J. S., Connolly, D. J., Giladi, T., Scicluna, B. J., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-02083-1 · Cited by 192 · see citing works
New antigens for multi-component blood-stage vaccines against Plasmodium falciparum malaria
Osier, F., Mackinnon, M., Crosnier, C., Fegan, G., Kamuyu, G., Wanaguru, M., Ogada, E., McDade, B., Rayner, J., Wright, G. J., et al. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3008705 · Cited by 171
Lau, C. K., Turner, L., Jespersen, J. S., Lowe, E., Petersen, B. O., Wang, C. W., Petersen, J. E., Lusingu, J., Theander, T., Lavstsen, T., et al. (2015) · Cell Host and Microbe · doi:10.1016/j.chom.2014.11.007 · Cited by 170 · see citing works
“The extracellular ectodomains of the PfEMP1 proteins contain 2–10 copies of two Plasmodium-specific domain types, the Duffy-binding-like (DBL) and cysteine-rich interdomain region (CIDR) domains (Baruch et al., 1995; Smith et al., 1995; Su et al., 1995; Gardner et al., 2002).”
BackgroundToenhake, C. G., Fraschka, S. A. K., Vijayabaskar, M. S., Westhead, D. R., van Heeringen, S., & Bártfai, R. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.03.007 · Cited by 198 · see citing works
Site-specific genome editing in Plasmodium falciparum using engineered zinc-finger nucleases
Straimer, J., Lee, M., Lee, A. H., Zeitler, B., Williams, A. E., Pearl, J. R., Zhang, L., Rebar, E. J., Gregory, P. D., Llinás, M., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2143 · Cited by 161 · see citing works
Knuepfer, E., Napiorkowska, M., van Ooij, C., & Holder, A. A. (2017) · Scientific Reports · doi:10.1038/s41598-017-03984-3 · Cited by 189 · see citing works
Broadbent, K. M., Broadbent, J. C., Ribacke, U., Wirth, D. F., Rinn, J. L., & Sabeti, P. C. (2015) · BMC Genomics · doi:10.1186/s12864-015-1603-4 · Cited by 180 · see citing works
“falciparum genome sequence was published in 2002 [14].”
BackgroundPlasmodium falciparum Erythrocyte Invasion: Combining Function with Immune Evasion
Wright, G. J., & Rayner, J. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1003943 · Cited by 165 · see citing works
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Structural determinants of the hydrogen peroxide permeability of aquaporins
Almasalmeh, A., Krenc, D., Wu, B., & Beitz, E. (2014) · The FEBS Journal · doi:10.1111/febs.12653 · Cited by 163 · see citing works
Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria
Otto, T. D., Gilabert, A., Crellen, T., Böhme, U., Arnathau, C., Sanders, M. J., Oyola, S. O., Okouga, A. P., Boundenga, L., Willaume, E., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0162-2 · Cited by 185 · see citing works
“Third, the ATS domains cluster tightly within Clade A.”
InfluentialSelf-citationSundararaman, S. A., Plenderleith, L. J., Liu, W., Loy, D. E., Learn, G. H., Li, Y., Shaw, K. S., Ayouba, A., Peeters, M., Speede, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms11078 · Cited by 156 · see citing works
Heidel, A. J., Lawal, H., Felder, M., Schilde, C., Helps, N. R., Tunggal, B., Rivero, F., John, U., Schleicher, M., Eichinger, L., et al. (2011) · Genome Research · doi:10.1101/gr.121137.111 · Cited by 155 · see citing works
“Several exceptional features were described, among them a high A/T nucleotide content, surpassed only by Plasmodium falciparum (Gardner et al. 2002) and extreme richness in transposons and other repetitive elements (Glöckner et al. 2001).”
BackgroundYang, R.-H., Su, J.-H., Shang, J.-J., Wu, Y.-Y., Li, Y., Bao, D., & Yao, Y.-J. (2018) · PLoS ONE · doi:10.1371/journal.pone.0206428 · Cited by 159
Vasquez, J.-J., Hon, C.-C., Vanselow, J. T., Schlösser, A., & Siegel, T. N. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1386 · Cited by 146 · see citing works
Mechanism of ribosome stalling during translation of a poly(A) tail
Chandrasekaran, V., Juszkiewicz, S., Choi, J., Puglisi, J. D., Brown, A., Shao, S., Ramakrishnan, V., & Hegde, R. S. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0331-x · Cited by 173 · see citing works
Oehring, S. C., Woodcroft, B. J., Moes, S., Wetzel, J., Dietz, O., Pulfer, A., Dekiwadia, C. D., Mäser, P., Flueck, C., Witmer, K., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-11-r108 · Cited by 148 · see citing works
“encloses and regulates a 23Mb genome encoding 5,400 genes on 14 linear chromosomes [5].”
BackgroundSelf-citationThe Prevalence and Impact of Model Violations in Phylogenetic Analysis
Naser-Khdour, S., Minh, B. Q., Zhang, W., Stone, E. A., & Lanfear, R. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz193 · Cited by 184 · see citing works
Extreme mutation bias and high AT content inPlasmodium falciparum
Hamilton, W. L., Claessens, A., Otto, T. D., Kekre, M., Fairhurst, R. M., Rayner, J. C., & Kwiatkowski, D. P. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1259 · Cited by 134 · see citing works
“The raw counts (and %) of observed indels from the 3D7 clone tree and BPS from all clone trees (3D7, HB3, Dd2, W2, KH1-01 and KH2-01) in exons, introns, and non-genic loci are shown, along with expected counts given a null hypothesis of the distribution being equal to the underlying genomic proportions (based on (2)).”
InfluentialPurine and Pyrimidine Pathways as Targets in Plasmodium falciparum
Cassera, M., Zhang, Y., Hazleton, K., & Schramm, V. (2011) · Current Topics in Medicinal Chemistry · doi:10.2174/156802611796575948 · Cited by 152 · see citing works
Efficient CRISPR-Cas9–mediated genome editing in Plasmodium falciparum
Wagner, J. C., Platt, R. J., Goldfless, S. J., Zhang, F., & Niles, J. C. (2014) · Nature Methods · doi:10.1038/nmeth.3063 · Cited by 220 · see citing works
Highly divergent mitochondrion-related organelles in anaerobic parasitic protozoa.
Makiuchi, T., & Nozaki, T. (2014) · Biochimie · doi:10.1016/j.biochi.2013.11.018 · Cited by 151 · see citing works
Galen, S. C., Borner, J., Martinsen, E. S., Schaer, J., Austin, C. C., West, C. J., & Perkins, S. L. (2018) · Royal Society Open Science · doi:10.1098/rsos.171780 · Cited by 162 · see citing works
“For instance, the genome of the virulent human malaria parasite Plasmodium falciparum has a GC content of approximately 19% [43], though GC content can be as high as 42% in another human-infecting species, Plasmodium vivax [44,45].”
BackgroundImmune evasion of Plasmodium falciparum by RIFIN via inhibitory receptors
Saito, F., Hirayasu, K., Satoh, T., Wang, C. W., Lusingu, J., Arimori, T., Shida, K., Palacpac, N., Itagaki, S., Iwanaga, S., et al. (2017) · Nature · doi:10.1038/nature24994 · Cited by 150 · see citing works
“The P. falciparum genome does not encode an MHC class I-like gene 15 .”
- Authors
- Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., Carlton, J. M., Pain, A., Nelson, K. E., Bowman, S., Paulsen, I. T., James, K., Eisen, J. A., Rutherford, K., Salzberg, S. L., Craig, A., Kyes, S., Chan, M.-S., Nene, V., Shallom, S. J., Suh, B., Peterson, J., Angiuoli, S., Pertea, M., Allen, J., Selengut, J., Haft, D., Mather, M. W., Vaidya, A. B., Martin, D. M. A., Fairlamb, A. H., Fraunholz, M. J., Roos, D. S., Ralph, S. A., McFadden, G. I., Cummings, L. M., Subramanian, G. M., Mungall, C., Venter, J. C., Carucci, D. J., Hoffman, S. L., Newbold, C., Davis, R. W., Fraser, C. M., & Barrell, B.
- Affiliations
- J. Craig Venter Institute (US)
- Corresponding author
- Gardner, Malcolm J.
- ORCID
- Gardner, Malcolm J.
- Hall, Neil
- Fung, Eula
- White, Owen
- Berriman, Matthew
- Hyman, Richard W.
- Carlton, Jane M.
- Pain, Arnab
- Paulsen, Ian T.
- Eisen, Jonathan A.
- Rutherford, Kim
- Salzberg, Steven L.
- Craig, Alister
- Nene, Vishvanath
- Pertea, Mihaela
- Allen, Jonathan
- Haft, Daniel
- Mather, Michael W.
- Vaidya, Akhil B.
- Martin, David M. A.
- Fairlamb, Alan H.
- Fraunholz, Martin J.
- Roos, David S.
- Ralph, Stuart A.
- McFadden, Geoffrey I.
- Mungall, Chris
- Venter, J. Craig
- Hoffman, Stephen L.
- Newbold, Chris
- Davis, Ronald W.
- Fraser, Claire M.
- Venue
- Nature
- Published
- 2002-10
- Volume
- 419
- Issue
- 6906
- Pages
- 498-511
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3836256
- OpenAlex
- W2019851585
- Cited by
- 4,407
- References
- 170
- Citations by year
- 2026: 68 · 2025: 107 · 2024: 112 · 2023: 107 · 2022: 154 · 2021: 151 · 2020: 148 · 2019: 140 · 2018: 150 · 2017: 160 · 2016: 183 · 2015: 166 · 2014: 213 · 2013: 191 · 2012: 211
- FWCI
- 272.18
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Discovery Research Portal (University of Dundee) (submittedVersion)
- Funders
- Burroughs Wellcome Fund
- Global Fund to Fight AIDS, Tuberculosis and Malaria
- Wellcome Trust (061524)
- Stanford Bio-X
- National Institute of Allergy and Infectious Diseases (R01AI028398)
- Medical Research and Materiel Command
- Naval Medical Research Center
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Malaria Research and Control
- Life Sciences › Immunology and Microbiology › Parasitology › Bird parasitology and diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Plasmodium falciparum, Plasmodium, genome sequence, nuclear genome, antigenic variation, subtelomeric regions, immune evasion, host-parasite interactions, apicoplast, isoprenoid metabolism, gene content, drug and vaccine targets
- MeSH terms
- Animals, DNA Repair, DNA Replication, Humans, Molecular Sequence Data, Plasmodium falciparum, Recombination, Genetic, Protozoan Proteins, DNA, Protozoan, Malaria, Falciparum, Sequence Analysis, DNA, Malaria Vaccines, Plastids, Genome, Protozoan, Evolution, Molecular, Proteome, Chromosome Structures, Membrane Transport Proteins
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