收稿日期: 2020-08-18
修回日期: 2021-01-15
网络出版日期: 2021-04-30
基金资助
江苏省公益类科研院所自主科研项目(BM2018020);江苏省“科教强卫工程”项目(BM2018020)
Research advance and application of whole-genome sequencing of Plasmodium
Received date: 2020-08-18
Revised date: 2021-01-15
Online published: 2021-04-30
Supported by
Jiangsu Provincial Department of Science and Technology(BM2018020);Jiangsu Provincial Project of Invigorating Health Care through Science, Technology and Education(BM2018020)
刘宏 , 刘耀宝 , 曹俊 . 疟原虫全基因组测序研究进展及其应用[J]. 中国寄生虫学与寄生虫病杂志, 2021 , 39(2) : 265 -270 . DOI: 10.12140/j.issn.1000-7423.2021.02.021
Malaria is an infectious disease caused by Plasmodium infection and one of the most important public health problems in the world. With the completion of human malaria parasite genome sequence and the development of sequencing technology, the whole-genome sequencing is becoming increasingly useful in determining parasite evolution, revealing epidemic characteristics, drug resistance surveillance, and genetic tracking. This paper reviews the advances in research on and application of the whole-genome sequencing technology for studies on Plasmodium.
Key words： Malaria; Plasmodium; Whole-genome sequencing
| [1] | Zhang L, Feng J, Xia ZG, et al. Analysis of epidemic characteristics and elimination of malaria in China in 2019[J]. Chin J Parasitol Parasit Dis, 2020,38(2):133-138. (in Chinese) |
| [1] | ( 张丽, 丰俊, 夏志贵, 等. 2019年全国疟疾疫情特征分析及消除工作进展[J]. 中国寄生虫学与寄生虫病杂志, 2020,38(2):133-138.) |
| [2] | Xu QL, Zhou HR, Qian MB, et al. Research progress on economic burden of malaria[J]. Chin J Parasitol Parasit Dis, 2020,38(6):749-752. (in Chinese) |
| [2] | ( 许秋利, 周鸿让, 钱门宝, 等. 疟疾经济负担研究进展[J]. 中国寄生虫学与寄生虫病杂志, 2020,38(6):749-752.) |
| [3] | World Health Organization. World malaria report 2019[R]. Geneva: World Health Organization, 2019. |
| [4] | Li SH, Li J, Gao LJ, et al. Application of fluorescence quantitative PCR in laboratory diagnosis of malaria[J]. Chin J Parasitol Parasit Dis, 2019,37(2):232-234. (in Chinese) |
| [4] | ( 李素华, 李静, 高丽君, 等. 荧光定量PCR在疟疾实验室诊断中的应用[J]. 中国寄生虫学与寄生虫病杂志, 2019,37(2):232-234.) |
| [5] | Li M, Xia ZG, Tang LH. Establishment and application of multiplex PCR system for detection of 4 species of human Plasmodium[J]. Chin J Parasitol Parasit Dis, 2015,33(2):91-95. (in Chinese) |
| [5] | ( 李美, 夏志贵, 汤林华. 检测4种人体疟原虫多重PCR体系的建立和应用[J]. 中国寄生虫学与寄生虫病杂志, 2015,33(2):91-95.) |
| [6] | Gardner MJ, Hall N, Fung E, et al. Genome sequence of the human malaria parasite Plasmodium falciparum[J]. Nature, 2002,419(6906):498-511. |
| [7] | Carlton JM, Adams JH, Silva JC, et al. Comparative genomics of the neglected human malaria parasite Plasmodium vivax[J]. Nature, 2008,455(7214):757-763. |
| [8] | Pain A, B?hme U, Berry AE, et al. The genome of the simian and human malaria parasite Plasmodium knowlesi[J]. Nature, 2008,455(7214):799-803. |
| [9] | Rutledge GG, B?hme U, Sanders M, et al. Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution[J]. Nature, 2017,542(7639):101-104. |
| [10] | Ansari HR, Templeton TJ, Subudhi AK, et al. Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species[J]. Int J Parasitol, 2016,46(11):685-696. |
| [11] | PlasmoDB: a functional genomic database formalaria parasites.[EB/OL]. (2008-10-31). [2020-03-08]. https://plasmodb.org. |
| [12] | Volkman SK, Sabeti PC DeCaprio D, et al. A genome-wide map of diversity in Plasmodium falciparum[J]. Nat Genet, 2007,39(1):113-119. |
| [13] | Su XZ, Lane KD, Xia L, et al. Plasmodium genomics and genetics: new insights into malaria pathogenesis, drug resistance, epidemiology, and evolution[J]. Clin Microbiol Rev, 2019,32(4):e00019-19. |
| [14] | Aurrecoechea C, Brestelli J, Brunk BP, et al. PlasmoDB: a functional genomic database for malaria parasites[J]. Nucl Acid Res, 2009,37(suppl 1):D539-D543. |
| [15] | Network TMGE. A global network for investigating the genomic epidemiology of malaria[J]. Nature, 2008,456(7223):732-737. |
| [16] | Neafsey DE, Galinsky K, Jiang RHY, et al. The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum[J]. Nat Genet, 2012,44(9):1046-1050. |
| [17] | Liu W, Sundararaman SA, Loy DE, et al. Multigenomic delineation of Plasmodium species of the Laverania subgenus infecting wild-living chimpanzees and gorillas[J]. Genome Biol Evol, 2016,8(6):1929-1939. |
| [18] | Liu W, Li Y, Learn GH, et al. Origin of the human malaria parasite Plasmodium falciparum in gorillas[J]. Nature, 2010,467(7314):420-425. |
| [19] | Otto TD, Gilabert A, Crellen T, et al. Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria[J]. Nat Microbiol, 2018,3(6):687-697. |
| [20] | Liu W, Li Y, Shaw KS, et al. African origin of the malaria parasite Plasmodium vivax[J]. Nat Commun, 2014,5:3346. |
| [21] | McManus KF, Taravella AM, Henn BM, et al. Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans[J]. PLoS Genet, 2017,13(3):e1006560. |
| [22] | Culleton R, Carter R. African Plasmodium vivax: distribution and origins[J]. Int J Parasitol, 2012,42(12):1091-1097. |
| [23] | Gilabert A, Otto TD, Rutledge GG, et al. Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution[J]. PLoS Biol, 2018,16(8):e2006035. |
| [24] | Arisue N, Hashimoto T, Kawai S, et al. Apicoplast phylogeny reveals the position of Plasmodium vivax basal to the Asian primate malaria parasite clade[J]. Sci Rep, 2019,9(1):7274. |
| [25] | de Oliveira TC, Rodrigues PT, Menezes MJ, et al. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax[J]. PLoS Neglected Trop Dis, 2017,11(7):e0005824. |
| [26] | Pearson RD, Amato R, Auburn S, et al. Genomic analysis of local variation and recent evolution in Plasmodium vivax[J]. Nat Genet, 2016,48(8):959-964. |
| [27] | Arisue N, Hashimoto T, Mitsui H, et al. The Plasmodium apicoplast genome: conserved structure and close relationship of P. ovale to rodent malaria parasites[J]. Mol Biol Evol, 2012,29(9):2095-2099. |
| [28] | Roh ME, Tessema SK, Murphy M, et al. High genetic diversity of Plasmodium falciparum in the low-transmission setting of the kingdom of eswatini[J]. J Infect Dis, 2019,220(8):1346-1354. |
| [29] | Chen XD, Ye R, Pan WQ. Study on flanking microsatellite polymorphism of Plasmodium falciparum K13 gene in China-Myanmar border and southeastern Thailand[J]. Chin J Parasitol Parasit Dis, 2017,35(3):209-212. (in Chinese) |
| [29] | ( 陈学迪, 叶润, 潘卫庆. 中缅边境及泰国东南地区恶性疟原虫K13基因侧翼微卫星多态性研究[J]. 中国寄生虫学与寄生虫病杂志, 2017,35(3):209-212.) |
| [30] | Pringle JC, Tessema S, Wesolowski A, et al. Genetic evidence of focal Plasmodium falciparum transmission in a pre-elimination setting in southern Province, Zambia[J]. J Infect Dis, 2019,219(8):1254-1263. |
| [31] | Manske M, Miotto O, Campino S, et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing[J]. Nature, 2012,487(7407):375-379. |
| [32] | Amambua-Ngwa A, Amenga-Etego L, Kamau E, et al. Major subpopulations of Plasmodium falciparum in sub-Saharan Africa[J]. Science, 2019,365(6455):813-816. |
| [33] | Shetty AC, Jacob CG, Huang F, et al. Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns[J]. Nat Commun, 2019,10(1):2665. |
| [34] | Amambua-Ngwa A, Jeffries D, Amato R, et al. Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from the Gambia[J]. Sci Rep, 2018,8:9687. |
| [35] | Duffy CW, Ba H, Assefa S, et al. Population genetic structure and adaptation of malaria parasites on the edge of endemic distribution[J]. Mol Ecol, 2017,26(11):2880-2894. |
| [36] | Hupalo DN, Luo ZP, Melnikov A, et al. Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax[J]. Nat Genet, 2016,48(8):953-958. |
| [37] | Noviyanti R, Coutrier F, Utami RA, et al. Contrasting transmission dynamics of co-endemic Plasmodium vivax and P. falciparum: implications for malaria control and elimination[J]. PLoS Negl Trop Dis, 2015,9(5):e0003739. |
| [38] | Chen SB, Wang Y, Kassegne K, et al. Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area[J]. BMC Genom, 2017,18(1):131. |
| [39] | Auburn S, Getachew S, Pearson RD, et al. Genomic analysis of Plasmodium vivax in southern Ethiopia reveals selective pressures in multiple parasite mechanisms[J]. J Infect Dis, 2019,220(11):1738-1749. |
| [40] | Tessema SK, Raman J, Duffy CW, et al. Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa[J]. Malar J, 2019,18:268. |
| [41] | Lu F, Culleton R, Zhang M, et al. Emergence of indigenous artemisinin-resistant Plasmodium falciparum in Africa[J]. N Engl J Med, 2017,376(10):991-993. |
| [42] | Daniels R, Volkman SK, Milner DA, et al. A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking[J]. Malar J, 2008,7:223. |
| [43] | Preston MD, Campino S, Assefa SA, et al. A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains[J]. Nat Commun, 2014,5:4052. |
| [44] | Baniecki ML, Faust AL, Schaffner SF, et al. Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections[J]. PLoS Negl Trop Dis, 2015,9(3):e0003539. |
| [45] | Rodrigues PT, Alves JM, Santamaria AM, et al. Using mitochondrial genome sequences to track the origin of imported Plasmodium vivax infections diagnosed in the United States[J]. Am J Trop Med Hyg, 2014,90(6):1102-1108. |
| [46] | Diez Benavente E, Campos M, Phelan J, et al. A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria[J]. PLoS Genet, 2020,16(2):e1008576. |
| [47] | Popovici J, Friedrich LR, Kim S, et al. Genomic analyses reveal the common occurrence and complexity of Plasmodium vivax relapses in Cambodia[J]. mBio, 2018,9(1):e01888-17. |
| [48] | Cowell AN, Valdivia HO, Bishop DK, et al. Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing[J]. Genome Med, 2018,10(1):52. |
| [49] | Gorobets NY, Sedash YV, Singh BK, et al. An overview of currently available antimalarials[J]. Curr Top Med Chem, 2017,17(19):2143-2157. |
| [50] | Thriemer K, Ley B, Bobogare A, et al. Challenges for achieving safe and effective radical cure of Plasmodium vivax: a round table discussion of the APMEN Vivax Working Group[J]. Malar J, 2017,16:141. |
| [51] | Blasco B, Leroy D, Fidock DA. Antimalarial drug resistance: linking Plasmodium falciparum parasite biology to the clinic[J]. Nat Med, 2017,23(8):917-928. |
| [52] | Amaratunga C, Lim P, Suon S, et al. Dihydroartemisinin-piperaquine resistance in Plasmodium falciparum malaria in Cambodia: a multisite prospective cohort study[J]. Lancet Infect Dis, 2016,16(3):357-365. |
| [53] | Mita T, Tanabe K, Kita K. Spread and evolution of Plasmodium falciparum drug resistance[J]. Parasitol Int, 2009,58(3):201-209. |
| [54] | Park DJ, Lukens AK, Neafsey DE, et al. Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite[J]. Proc Natl Acad Sci USA, 2012,109(32):13052-13057. |
| [55] | Cheeseman IH, Miller BA, Nair S, et al. A major genome region underlying artemisinin resistance in malaria[J]. Science, 2012,336(6077):79-82. |
| [56] | Takala-Harrison S, Clark TG, Jacob CG, et al. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia[J]. Proc Natl Acad Sci USA, 2013,110(1):240-245. |
| [57] | Miotto O, Almagro-Garcia J, Manske M, et al. Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia[J]. Nat Genet, 2013,45(6):648-655. |
| [58] | Ariey F, Witkowski B, Amaratunga C, et al. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria[J]. Nature, 2014,505(7481):50-55. |
| [59] | Ménard D, Khim N, Beghain J, et al. A worldwide map of Plasmodium falciparum K13-propeller polymorphisms[J]. N Engl J Med, 2016,374(25):2453-2464. |
| [60] | Hamilton WL Amato R van der Pluijm RW, et al. Evolution and expansion of multidrug-resistant malaria in Southeast Asia: a genomic epidemiology study[J]. Lancet Infect Dis, 2019,19(9):943-951. |
| [61] | van der Pluijm RW, Imwong M, Chau NH, et al. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study[J]. Lancet Infect Dis, 2019,19(9):952-961. |
| [62] | Cowell AN, Istvan ES, Lukens AK, et al. Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics[J]. Science, 2018,359(6372):191-199. |
| [63] | Winter DJ, Pacheco MA, Vallejo AF, et al. Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia[J]. PLoS Negl Trop Dis, 2015,9(12):e0004252. |
| [64] | Shen HM, Chen SB, Wang Y, et al. Genome-wide scans for the identification of Plasmodium vivax genes under positive selection[J]. Malar J, 2017,16:238. |
| [65] | Auburn S, Marfurt J, Maslen G, et al. Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing[J]. PLoS One, 2013,8(1):e53160. |
| [66] | Zhong D, Koepfli C, Cui L, et al. Molecular approaches to determine the multiplicity of Plasmodium infections[J]. Malar J, 2018,17:172. |
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