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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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“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 Plasmodium spp (2005) · cites this paper as [11]
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“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 Plasmodium spp (2005) · cites this paper as [11]
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“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 Plasmodium spp (2005) · cites this paper as [11]
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Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4315 · Cited by 12,654
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
Emanuelsson, O., Nielsen, H., Brunak, S., & von Heijne, G. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3903 · Cited by 4,419
The Pfam protein families database
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp985 · Cited by 2,694
The Genome Sequence of the Malaria Mosquito Anopheles gambiae
Holt, R. A., Subramanian, G., Halpern, A. L., Sutton, G. G., Charlab, R., Nusskern, D. R., Wincker, P., Clark, A. G., Ribeiro, J. M. C., Wides, R., et al. (2002) · Science · doi:10.1126/science.1076181 · Cited by 2,025
Self-citationWood, R., Mitchell, M., Sgouros, J., & Lindahl, T. (2001) · Science · doi:10.1126/science.1056154 · Cited by 1,719
The genome sequence of Schizosaccharomyces pombe
Wood, V., Gwilliam, R., Rajandream, M.-A., Lyne, M. H., Lyne, R., Stewart, A., SGOUROS, J. G., Peat, N., Hayles, J., Baker, S. G., et al. (2002) · Nature · doi:10.1038/nature724 · Cited by 1,671
Self-citationComputational Method to Predict Mitochondrially Imported Proteins and their Targeting Sequences
Claros, M. G., & Vincens, P. (1996) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1996.00779.x · Cited by 1,650
Flagged first, then by citations
11 of the 170 references couldn’t be matched to a known paper.
Research works printed but not linked: 8
- Louis, E. J., Naumova, E. S., Lee, A., Naumov, G. & Haber, J. E. The chromosome end in yeast: its mosaic nature and influence on recombinational dynamics. Genetics 136, 789–802 (1994) · DOI
- DeRocher, A., Hagen, C. B., Froehlich, J. E., Feagin, J. E. & Parsons, M. Analysis of targeting sequences demonstrates that trafficking to the Toxoplasma gondii plastid branches off the secretory system. J. Cell Sci. 113 (Part 22), 3969–3977 (2000) · DOI
- Vaidya, A. B. in Malaria: Parasite Biology, Pathogenesis, and Protection (ed. Sherman, I. W.) 355–368 (ASM, Washington DC, 1998)
- Sherman, I. W. in Malaria: Parasite Biology, Pathogenesis, and Protection (ed. Sherman, I. W.) 177–184 (ASM, Washington DC, 1998)
- Vaidya, A. B., McIntosh, M. T. & Srivastava, I. K. Membrane Structure in Disease and Drug Therapy (ed. Zimmer, G.) (Marcel Dekker, New York, 2000)
- Rohdich, F. et al. Biosynthesis of terpenoids. 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) from Plasmodium falciparum. Eur. J. Biochem. 268, 3190–3197 (2001) · DOI
- Adisa, A., Albano, F. R., Reeder, J., Foley, M. & Tilley, L. Evidence for a role for a Plasmodium falciparum homologue of Sec31p in the export of proteins to the surface of malaria parasite-infected erythrocytes. J. Cell Sci. 114, 3377–3386 (2001) · DOI
- Nielsen, H., Engelbrecht, J., Brunak, S. & von Heijne, G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10, 1–6 (1997) · DOI
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Quail, M., Smith, M. E., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P., & Gu, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-341 · Cited by 2,031
“4% [14], we use it as one of our test genomes, representing a significant challenge to most sequencing technologies.”
MethodA vision for the future of genomics research
Collins, F. S., Green, E. D., Guttmacher, A. E., Guyer, M. S., & on behalf of the US National Human Genome Research Institute (2003) · Nature · doi:10.1038/nature01626 · Cited by 1,752
The genome of the social amoeba Dictyostelium discoideum
Eichinger, L., Pachebat, J. A., Glöckner, G., Rajandream, M.-A., Sucgang, R., Berriman, M., Song, J., Olsen, R., Szafranski, K., Xu, Q., et al. (2005) · Nature · doi:10.1038/nature03481 · Cited by 1,351
Self-citationAnalyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Aird, D., Ross, M. G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D. B., Nusbaum, C., & Gnirke, A. (2011) · Genome Biology · doi:10.1186/gb-2011-12-2-r18 · Cited by 1,174
Circlator: automated circularization of genome assemblies using long sequencing reads
Hunt, M., Silva, N. H. D., Otto, T. D., Parkhill, J., Keane, J. A., & Harris, S. R. (2015) · Genome biology · doi:10.1186/s13059-015-0849-0 · Cited by 1,181
“We evaluated the circularization tools using data from the reference strain 3D7 [18].”
MethodZhang, M., Wang, C. C. Q., Otto, T. D., Oberstaller, J., Liao, X., Adapa, S. R., Udenze, K., Bronner, I. F., Casandra, D. R., Mayho, M., et al. (2018) · Science · doi:10.1126/science.aap7847 · Cited by 919
“falciparum genome, a substantial fraction of its genome still lacks functional annotation (3).”
Protection Against Malaria by Intravenous Immunization with a Nonreplicating Sporozoite Vaccine
Seder, R. A., Chang, L.-J., Enama, M. E., Zephir, K. L., Sarwar, U. N., Gordon, I. J., Holman, L. A., James, E. R., Billingsley, P. F., Gunasekera, A. M., et al. (2013) · Science · doi:10.1126/science.1241800 · Cited by 764
Self-citationCowman, A. F., Healer, J., Marapana, D. S., & Marsh, K. (2016) · Cell · doi:10.1016/j.cell.2016.07.055 · Cited by 972
Salanti, A., Staalsoe, T., Lavstsen, T., Jensen, A. T. R., Sowa, M. P. K., Arnot, D. E., Hviid, L., & Theander, T. G. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03570.x · Cited by 702
Malaria: progress, perils, and prospects for eradication
Greenwood, B. M., Fidock, D. A., Kyle, D. E., Kappe, S. H. I., Alonso, P. L., Collins, F. H., & Duffy, P. E. (2008) · Journal of Clinical Investigation · doi:10.1172/jci33996 · Cited by 709
Douglas, A. D., Williams, A. R., Illingworth, J., Kamuyu, G., Biswas, S., Goodman, A., Wyllie, D., Crosnier, C., Miura, K., Wright, G. J., et al. (2011) · Nature Communications · doi:10.1038/ncomms1615 · Cited by 666
Evidence for the Involvement of VAR2CSA in Pregnancy-associated Malaria
Salanti, A., Dahlbäck, M., Turner, L., Nielsen, M. A., Barfod, L., Magistrado, P., Jensen, A. T. R., Lavstsen, T., Ofori, M. F., Marsh, K., et al. (2004) · The Journal of Experimental Medicine · doi:10.1084/jem.20041579 · Cited by 604
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
Manske, M., Miotto, O., Campino, S. G., Auburn, S., Garcia, J. A., Maslen, G. L., O’Brien, J., DJIMDÉ, A. A., Doumbo, O. K., Zongo, I., et al. (2012) · Nature · doi:10.1038/nature11174 · Cited by 469
Self-citationDraft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure.
Shoguchi, E., Shinzato, C., Kawashima, T., Gyoja, F., Mungpakdee, S., Koyanagi, R., Takeuchi, T., Hisata, K., Tanaka, M., Fujiwara, M., et al. (2013) · Current Biology · doi:10.1016/j.cub.2013.05.062 · Cited by 522
The evolution of signalling pathways in animal development
Pires-daSilva, A., & Sommer, R. J. (2003) · Nature Reviews Genetics · doi:10.1038/nrg977 · Cited by 466
Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes
Oyola, S. O., Otto, T. D., Gu, Y., Maslen, G. L., Manske, M., Campino, S. G., Turner, D., MacInnis, B. L., Kwiatkowski, D. P., Swerdlow, H., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-1 · Cited by 654
“falciparum genome is very AT-rich; coding regions have a mean AT content of more than 75%, with up to 100% in intergenic and non-coding regions [2].”
BackgroundNaccache, S. N., Federman, S., Veeraraghavan, N., Zaharia, M., Lee, D., Samayoa, E., Bouquet, J., Greninger, A. L., Luk, K.-C., Enge, B., et al. (2014) · Genome Research · doi:10.1101/gr.171934.113 · Cited by 460
“…in the Democratic Republic ofthe Congo (DRC), Africa, wasanalyzed by unbiased NGS. NGSreads identified as Plasmodium bySURPI are mappedtothe 14chromosomes of Plasmodium falciparum clone 3D7, including multiple hits to telomeric ends by reads corresponding to the var gene (Gardner et al. 2002).”
BackgroundRogozin, I. B., Wolf, Y. I., Sorokin, A. V., Mirkin, B. G., & Koonin, E. V. (2003) · Current Biology · doi:10.1016/s0960-9822(03)00558-x · Cited by 445
Mathematical models of malaria - a review
Mandal, S., Sarkar, R. R., & Sinha, S. (2011) · Malaria Journal · doi:10.1186/1475-2875-10-202 · Cited by 409
“falciparum were sequenced in 2002 [10,11].”
Library preparation methods for next-generation sequencing: Tone down the bias
van Dijk, E., Jaszczyszyn, Y., & Thermes, C. (2014) · Experimental Cell Research · doi:10.1016/j.yexcr.2014.01.008 · Cited by 436
“This effect severely complicates the sequencing of extremely AT-rich genomes, such as that of a human malaria parasite (Plasmodium falciparum—average AT content, 80% [8]), or extremely GC-rich genomes such as the herpes B virus (average GC content, 75% [9]), or profiling of highly GC-rich CpG islands of cancer genomes.”
BackgroundTreeck, M., Sanders, J. L., Elias, J. E., & Boothroyd, J. C. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.09.004 · Cited by 374
“falciparum proteome as a whole (Gardner et al., 2002) and has been presumed to reflect forces driving the P.”
BackgroundResultInfluentialA cascade of DNA-binding proteins for sexual commitment and development in Plasmodium
Sinha, A., Hughes, K. R., Modrzynska, K., Otto, T. D., Pfander, C., Dickens, N. J., Religa, A. A., Bushell, E., Graham, A., Cameron, R., et al. (2014) · Nature · doi:10.1038/nature12970 · Cited by 435
“Lines generated in this way were designated m(7,8,9)mxClx, indicating the mouse and clone number identifiers from the negative selection process.”
BackgroundSelf-citationHofmann, N., Mwingira, F., Shekalaghe, S., Robinson, L. J., Mueller, I., & Felger, I. (2015) · PLOS Medicine · doi:10.1371/journal.pmed.1001788 · Cited by 413
López-Barragán, M. J., Lemieux, J., Quiñones, M., Williamson, K., Molina-Cruz, A., Cui, K.-R., Barillas-Mury, C., Zhao, K.-J., & Su, X.-Z. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-587 · Cited by 373
“To facilitate development of drugs and vaccines to control malaria and to better understand the biology of the parasite, the genome of the 3D7 strain was sequenced and published in 2002 [2], which constitutes a significant achievement in malaria research.”
BackgroundCowman, A., Berry, D., & Baum, J. (2012) · doi:10.1083/jcb.201206112 · Cited by 369
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].”
Backgrounddel 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
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 306
Crompton, P. D., Moebius, J., Portugal, S., Waisberg, M., Hart, G. T., Garver, L. S., Miller, L. H., Barillas-Mury, C. V., & Pierce, S. K. (2014) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032713-120220 · Cited by 341
“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…”
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
Designing 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 281
“With the sequencing of the parasite genomes [3-5], new potential drug targets have emerged.”
BackgroundOn the Cytoadhesion of Plasmodium vivax –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
Staalsoe, T., Shulman, C. E., Bulmer, J. N., Kawuondo, K., Marsh, K., & Hviid, L. (2004) · The Lancet · doi:10.1016/s0140-6736(03)15386-x · Cited by 288
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
Self-citationReal-Time PCR for Detection and Identification of Plasmodium 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
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
“…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 269
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
Lorenzi, H., Khan, A., Behnke, M. S., Namasivayam, S., Swapna, L. S., Hadjithomas, M., Karamycheva, S. A., Pinney, D. F., Brunk, B. P., Ajioka, J. W., et al. (2016) · Nature Communications · doi:10.1038/ncomms10147 · Cited by 281
“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. A., & Grant, G. R. (2016) · Nature Methods · doi:10.1038/nmeth.4106 · Cited by 289
“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., 藤田, 佳., Nakayashiki, H., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002147 · Cited by 265
“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 269
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 257
Swart, E. C., Bracht, J. R., Magrini, V. J., Minx, P. J., Chen, X., Zhou, Y., Khurana, J. S., Goldman, A. D., Nowacki, M., Schotanus, K., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001473 · Cited by 232
“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 224
“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
Ngô, L., Okogun, J. I., & Folk, W. R. (2013) · Natural Product Reports · doi:10.1039/c3np20120a · Cited by 254
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 247
“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
“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
Tabor, A. E., & Rodriguez-Valle, M. (2015) · Ticks and Tick-borne Diseases · doi:10.1016/j.ttbdis.2015.12.012 · Cited by 244
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
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
“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
“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 241
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
“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 246
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
Viebig, N. K., Gamain, B., Scheidig, C., Lépolard, C., Przyborski, J., Lanzer, M., Gysin, J., & Scherf, A. (2005) · The EMBO Reports · doi:10.1038/sj.embor.7400466 · Cited by 201
Ediriweera, M. K., Tennekoon, K. H., & Samarakoon, S. R. (2017) · Evidence-based Complementary and Alternative Medicine · doi:10.1155/2017/6949835 · Cited by 216
“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
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
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
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
“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. W., Dillman, T., Kannan, N., Doerig, C., Chakrabarti, R., Gygi, S. P., et al. (2013) · Journal of Proteome Research · doi:10.1021/pr400394g · Cited by 159
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
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
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
“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
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
“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 183
“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 178
“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
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 214
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 197
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. D., Petersen, B., Wang, C. W., Petersen, J. E. V., Lusingu, J., Theander, T. G., Lavstsen, T., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.007 · Cited by 192
“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
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
Knuepfer, E., Napiorkowska, M., van Ooij, C., & Holder, A. A. (2017) · Scientific Reports · doi:10.1038/s41598-017-03984-3 · Cited by 185
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
“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
Trimnell, A. R., Kraemer, S. M., Mukherjee, S., Phippard, D. J., Janes, J. H., Flamoe, E., Su, X.-Z., Awadalla, P., & Smith, J. D. (2006) · Molecular and Biochemical Parasitology · doi:10.1016/j.molbiopara.2006.03.012 · Cited by 165
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
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 187
“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
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 163
“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 154
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
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
“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 188
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 139
“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
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 227
Highly divergent mitochondrion-related organelles in anaerobic parasitic protozoa
Makiuchi, T., & Nozaki, T. (2013) · Biochimie · doi:10.1016/j.biochi.2013.11.018 · Cited by 152
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 168
“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].”
Background
Metadata
- 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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