恶性疟原虫PfAP2-I基因编码区遗传多态与种间进化研究

doi:10.20199/j.issn.1672-2302.2026.03.002

摘要/Abstract

摘要：

目的分析恶性疟原虫PfAP2-I基因编码区在不同地理种群中的遗传多样性、群体分化、群体遗传结构及跨物种进化特征，为阐明其关键功能区的保守性和功能约束提供依据。方法从PlasmoDB和Pf3k项目下载PfAP2-I参考基因及群体基因组数据，构建来自13个国家的PfAP2-I编码区参考基因序列数据集，采用MEGA、DnaSP、KaKs_Calculator、Arlequin、STRUCTURE和NETWORK等软件分析其遗传多样性、选择压力、群体分化、群体结构及单倍型网络，并基于直系同源基因构建跨物种系统发育树。结果共纳入13个国家390条PfAP2-I基因编码区序列，编码区全长4 794 bp。各国样本单倍型数为5~18，其中孟加拉国样本最多（18个），缅甸最少（5个）；单倍型多样性为0.506~0.943。核苷酸多样性整体较低，最大值为0.013，主要分布于非DNA结合结构域，而3个DNA结合结构域中未见明显多样性峰值。各国样本Tajima’s D值均小于0。大多数国家样本Ka/Ks值小于1。F_ST、单倍型网络和群体结构分析均显示，非洲与东南亚种群之间存在较明显分化。跨物种系统发育树显示，不同疟原虫物种AP2-I基因分支清晰，并呈现一定宿主相关聚类特征。结论 PfAP2-I基因编码区整体较为保守，关键DNA结合相关区域保守性更高，并存在一定地理分化特征，提示该基因可能受到较强功能约束。

关键词: 恶性疟原虫, PfAP2-I基因编码区, 遗传多样性, 种群分化, 种间进化

Abstract:

Objective To investigate the genetic diversity, population differentiation, population genetic structure and interspecific evolutionary patterns of the PfAP2-I gene coding sequence (CDS) in Plasmodium falciparum from different geographic regions,so as to provide evidences for elucidating the conservation and functional constraints of its key functional domains. Methods The PfAP2-I reference sequence and population genomic data were downloaded from PlasmoDB and the Pf3k project, and a CDS dataset of PfAP2-I from 13 countries was constructed. Software MEGA, DnaSP, KaKs_Calculator, Arlequin, STRUCTURE and NETWORK were applied to analyze genetic diversity, selection pressure, population differentiation, population structure and haplotype networks. Furthermore, an interspecific phylogenetic tree was reconstructed based on orthologous genes. Results A total of 390 PfAP2-I gene CDS from 13 countries were included, with a CDS length of 4 794 bp. The number of haplotypes ranged from 5 to 18 among the samples from different countries, with the highest count measured in the samples from Bangladesh (18 haplotypes) and the lowest in samples from Myanmar (5 haplotypes). Haplotype diversity varied between 0.506 and 0.943. The overall nucleotide diversity was low, with a maximum value of 0.013, predominantly located outside the DNA-binding domains, and no obvious diversity peaks were observed within the three DNA-binding domains. Tajima’s D values were below zero in all populations. Ka/Ks values were below 1 for samples from most countries. Analyses of F_ST, haplotype network and population structure all showed evident differentiation between African and Southeast Asian populations. The interspecific phylogenetic tree showed clear clustering of AP2-I genes among different Plasmodium species, with a certain degree of host-related clustering. Conclusion The CDS of PfAP2-I gene is relatively conserved,with higher conservation in the key DNA-binding related regions and certain properties of geographical differentiation, suggesting that this gene may be under strong functional constraint.

Key words: Plasmodium falciparum, PfAP2-I coding sequence, Genetic diversity, Population differentiation, Interspecific evolution

中图分类号:

R382.3+1

段仪雯, 陈绅波, 陈军虎, 沈海默. 恶性疟原虫PfAP2-I基因编码区遗传多态与种间进化研究[J]. 热带病与寄生虫学, 2026, 24(3): 135-141.

DUAN Yiwen, CHEN Shenbo, CHEN Junhu, SHEN Haimo. Genetic polymorphism and interspecific evolution of the PfAP2-I gene coding sequence in Plasmodium falciparum[J]. Journal of Tropical Diseases and Parasitology, 2026, 24(3): 135-141.

图/表 7

图1

表1

图2

表2

图3

表3

图4

参考文献 38

[1]	Fikadu M, Ashenafi E. Malaria: an overview[J]. Infect Drug Resist, 2023, 16:3339-3347. doi: 10.2147/IDR.S405668 pmid: 37274361
[2]	Li QL, Liu T, Lv KY, et al. Malaria: past, present, and future[J]. Signal Transduct Target Ther, 2025, 10:188.
[3]	Venkatesan P. WHO world malaria report 2024[J]. Lancet Microbe, 2025, 6(4):101073. doi: 10.1016/j.lanmic.2025.101073 URL
[4]	Balmith M, Basson C, Brand SJ. The malaria burden: a South African perspective[J]. J Trop Med, 2024, 2024:6619010.
[5]	Weiss DJ, Dzianach PA, Saddler A, et al. Mapping the global prevalence, incidence, and mortality of Plasmodium falciparum and Plasmodium vivax malaria, 2000-22: a spatial and temporal modelling study[J]. Lancet, 2025, 405(10483):979-990. doi: 10.1016/S0140-6736(25)00038-8 URL
[6]	Tseha ST. Plasmodium species and drug resistance[M]. London: Intech Open, 2021.
[7]	Cowman AF, Berry D, Baum J. The cellular and molecular basis for malaria parasite invasion of the human red blood cell[J]. J Cell Biol, 2012, 198(6):961-971. doi: 10.1083/jcb.201206112 pmid: 22986493
[8]	Weiss GE, Gilson PR, Taechalertpaisarn T, et al. Revealing the sequence and resulting cellular morphology of receptor-ligand interactions during Plasmodium falciparum invasion of erythrocytes[J]. PLoS Pathog, 2015, 11(2):e1004670. doi: 10.1371/journal.ppat.1004670 URL
[9]	Modrzynska K, Pfander C, Chappell L, et al. A knockout screen of ApiAP2 genes reveals networks of interacting transcriptional regulators controlling the Plasmodium life cycle[J]. Cell Host Microbe, 2017, 21(1):11-22. doi: S1931-3128(16)30514-5 pmid: 28081440
[10]	Balaji S, Babu MM, Iyer LM, et al. Discovery of the principal specific transcription factors of Api complexa and their implication for the evolution of the AP2-integrase DNA binding domains[J]. Nucleic Acids Res, 2005, 33(13):3994-4006. pmid: 16040597
[11]	Le Berre M, Tubiana T, Reuterswärd Waldner P, et al. Structural characterization of the ACDC domain from ApiAP2 proteins, a potential molecular target against api complexan parasites[J]. Acta Crystallogr D Struct Biol, 2025, 81(Pt 1):38-48. doi: 10.1107/S2059798324012518 URL
[12]	Painter HJ, Campbell TL, Llinás M. The Api complexan AP2 family: integral factors regulating Plasmodium development[J]. Mol Biochem Parasitol, 2011, 176(1):1-7. doi: 10.1016/j.molbiopara.2010.11.014 URL
[13]	Tamura K, Stecher G, Peterson D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12):2725-2729. doi: 10.1093/molbev/mst197 pmid: 24132122
[14]	Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets[J]. Mol Biol Evol, 2017, 34(12):3299-3302. doi: 10.1093/molbev/msx248 pmid: 29029172
[15]	Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions[J]. Mol Biol Evol, 1986, 3(5):418-426. doi: 10.1093/oxfordjournals.molbev.a040410 pmid: 3444411
[16]	Wang DP, Zhang YB, Zhang Z, et al. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies[J]. Genom Proteom Bioinform, 2010, 8(1):77-80. doi: 10.1016/S1672-0229(10)60008-3 URL
[17]	Yang Z, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models[J]. Mol Biol Evol, 2000, 17(1):32-43. doi: 10.1093/oxfordjournals.molbev.a026236 pmid: 10666704
[18]	Excoffier L, Lischer HEL. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows[J]. Mol Ecol Resour, 2010, 10(3):564-567. doi: 10.1111/j.1755-0998.2010.02847.x pmid: 21565059
[19]	Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study[J]. Mol Ecol, 2005, 14(8):2611-2620. doi: 10.1111/j.1365-294X.2005.02553.x pmid: 15969739
[20]	Earl DA, VonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method[J]. Conserv Genet Resour, 2012, 4(2):359-361. doi: 10.1007/s12686-011-9548-7 URL
[21]	Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies[J]. Mol Biol Evol, 1999, 16(1):37-48. doi: 10.1093/oxfordjournals.molbev.a026036 pmid: 10331250
[22]	Carrington E, Cooijmans RHM, Keller D, et al. The ApiAP2 factor PfAP2-HC is an integral component of heterochromatin in the malaria parasite Plasmodium falciparum[J]. iScience, 2021, 24(5):102444. doi: 10.1016/j.isci.2021.102444 URL
[23]	Campbell TL, De Silva EK, Olszewski KL, et al. Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite[J]. PLoS Pathog, 2010, 6(10):e1001165. doi: 10.1371/journal.ppat.1001165 URL
[24]	Russell TJ, De Silva EK, Crowley VM, et al. Inhibitors of ApiAP2 protein DNA binding exhibit multistage activity against Plasmodium parasites[J]. PLoS Pathog, 2022, 18(10):e1010887. doi: 10.1371/journal.ppat.1010887 URL
[25]	Shang XM, Wang CH, Fan YT, et al. Genome-wide landscape of ApiAP2 transcription factors reveals a heterochromatin-associated regulatory network during Plasmodium falciparum blood-stage development[J]. Nucleic Acids Res, 2022, 50(6):3413-3431. doi: 10.1093/nar/gkac176 URL
[26]	Subudhi AK, Green JL, Satyam R, et al. DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages[J]. Nat Microbiol, 2023, 8(11):2154-2169. doi: 10.1038/s41564-023-01497-6 pmid: 37884813
[27]	Jeninga MD, Quinn JE, Petter M. ApiAP2 transcription factors in api complexan parasites[J]. Pathogens, 2019, 8(2):47. doi: 10.3390/pathogens8020047 URL
[28]	郑雨昕, 张义伟, 姜宁. 恶性疟原虫ApiAP2蛋白质家族研究进展[J]. 畜牧兽医学报, 2022, 53(5):1354-1363. doi: 10.11843/j.issn.0366-6964.2022.05.004
[29]	Pacheco MA, Matta NE, Valkiunas G, et al. Mode andrate of evolution of haemosporidian mitochondrial genomes: timing the radiation of avian parasites[J]. Mol Biol Evol, 2018, 35(2):383-403. doi: 10.1093/molbev/msx285 URL
[30]	Alemneh T, Molla W, Abdela S, et al. Avian malaria: an in-depth overview on its biology, epidemiology, pathogenesis, clinical features, economic impacts, diagnostic, treatment and control strategies[J]. J Parasit Dis, 2025:1-40.
[31]	Galinski MR. Systems biology of malaria explored with nonhuman Primates[J]. Malar J, 2022, 21(1):177. doi: 10.1186/s12936-022-04199-2
[32]	De Niz M, Heussler VT. Rodent malaria models: insights into human disease and parasite biology[J]. Curr Opin Microbiol, 2018, 46:93-101. doi: S1369-5274(17)30250-3 pmid: 30317152
[33]	Singhal R, Prata IO, Bonnell VA, et al. Unraveling the complexities of ApiAP2 regulation in Plasmodium falciparum[J]. Trends Parasitol, 2024, 40(11):987-999. doi: 10.1016/j.pt.2024.09.007 pmid: 39419713
[34]	Smith JD, Gamain B, Baruch DI, et al. Decoding the language of var genes and Plasmodium falciparum sequestration[J]. Trends Parasitol, 2001, 17(11):538-545. pmid: 11872399
[35]	Kraemer SM, Kyes SA, Aggarwal G, et al. Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates[J]. BMC Genomics, 2007, 8:45. pmid: 17286864
[36]	Lau CKY, Turner L, Jespersen JS, et al. Structural conservation despite huge sequence diversity allows EPCR binding by the PfEMP1 family implicated in severe childhood malaria[J]. Cell Host Microbe, 2015, 17(1):118-129. doi: 10.1016/j.chom.2014.11.007 pmid: 25482433
[37]	Frech C, Chen NS. Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis[J]. BMC Genomics, 2013, 14:427. doi: 10.1186/1471-2164-14-427 pmid: 23805789
[38]	Niang M, Bei AK, Madnani KG, et al. STEVOR is a Plasmodium falciparum erythrocyte binding protein that mediates merozoite invasion and rosetting[J]. Cell Host Microbe, 2014, 16(1):81-93. doi: 10.1016/j.chom.2014.06.004 URL

样本来源	样本数（条）	K 值	H 值	Hd±SD 值	S 值	Sv 值	Sp 值	η 值	π值	Ka值	Ks值	Ka/Ks值	P值	D^a值	D^b值	F^c值
孟加拉国	30	3.092	18	0.943±0.027	13	0	13	13	0.000 64	0.000 69	0.000 32	2.185	0.167 86	-0.191	1.497	1.137
柬埔寨	30	1.014	8	0.651±0.086	7	3	4	7	0.000 21	0.000 24	0.000 24	0.995	0.962 56	-1.259	-0.817	-1.108
刚果（金）	30	1.172	9	0.717±0.075	8	4	4	8	0.000 24	0.000 20	0.000 32	0.639	0.460 29	-1.274	-1.211	-1.436
冈比亚	30	0.841	6	0.579±0.095	5	1	4	5	0.000 18	0.000 14	0.000 48	0.284	0.024 34	-0.909	0.268	-0.093
加纳	30	1.175	8	0.692±0.071	8	3	5	8	0.000 25	0.000 19	0.000 63	0.293	0.010 83	-1.271	-0.577	-0.920
几内亚	30	1.862	12	0.798±0.068	16	12	4	16	0.000 39	0.000 38	0.000 44	0.871	0.613 09	-1.830	-2.927	-3.030
老挝	30	2.011	14	0.853±0.056	14	5	9	14	0.000 42	0.000 44	0.000 24	1.847	0.458 83	-1.438	-0.559	-0.978
马拉维	30	2.607	14	0.752±0.084	17	3	14	17	0.000 54	0.000 57	0.000 63	0.905	0.838 42	-1.343	0.513	-0.087
马里	30	1.168	9	0.662±0.089	8	4	4	8	0.000 24	0.000 20	0.000 48	0.426	0.080 62	-1.281	-1.211	-1.439
缅甸	30	1.044	5	0.540±0.099	5	1	4	5	0.000 22	0.000 30	0		0.007 41	-0.472	0.268	0.057
塞内加尔	30	1.584	10	0.639±0.099	14	8	6	14	0.000 33	0.000 33	0.000 28	1.186	0.988 24	-1.841	-1.807	-2.132
泰国	30	1.046	7	0.685±0.061	7	3	4	7	0.000 22	0.000 22	0.000 16	1.385	0.944 89	-1.206	-0.817	-1.089
越南	30	0.768	6	0.506±0.106	7	4	3	7	0.000 16	0.000 15	0.000 24	0.639	0.354 75	-1.671	-1.513	-1.820

样本来源	冈比亚	几内亚	泰国	加纳	柬埔寨	马里	孟加拉国	马拉维	越南	缅甸	老挝	刚果（金）
几内亚	0.0252
泰国	0.670 8	0.579 5
加纳	0.007 4	0.018 3	0.632 3
柬埔寨	0.659 0	0.564 9	0.103 6	0.618 0
马里	-0.015 9	0.012 0	0.637 7	-0.011 7	0.624 4
孟加拉国	0.300 4	0.268 6	0.123 3	0.274 9	0.117 7	0.284 2
马拉维	0.012 9	0.002 5	0.519 4	0.026 5	0.503 9	0.007 8	0.239 0
越南	0.701 3	0.598 0	0.064 0	0.657 5	-0.004 7	0.663 7	0.121 0	0.534 2
缅甸	0.584 2	0.493 2	0.065 3	0.546 7	0.070 4	0.551 7	0.050 5	0.429 6	0.056 5
老挝	0.565 1	0.493 6	0.070 4	0.529 6	0.052 0	0.537 9	0.084 3	0.444 6	0.027 5	0.071 1
刚果（金）	-0.009 1	0.001 8	0.637 3	0.001 7	0.623 9	-0.018 5	0.285 6	0.006 6	0.662 4	0.550 8	0.534 2
塞内加尔	0.004 2	0.004 7	0.594 4	0.017 9	0.581 0	0.004 6	0.260 2	0.004 3	0.617 1	0.501 1	0.507 9	0.004 5

序号	物种名称	参考株（系）	基因编号	宿主类型
1	P. falciparum	3D7	PF3D7_1007700	人类
2	P. inui	San Antonio 1	C922_02199t30	非人灵长类，猕猴为主
3	P. adleri	G01	PADL01_1006200t36	非人灵长类，大猩猩为主
4	P. billcollinsi	G01	PBILCG01_1007100	非人灵长类，黑猩猩为主
5	P. blacklocki	G01	PBLACG01_1005800t36	非人灵长类，大猩猩为主
6	P. chabaudi	chabaudi	PCHAS_1206600	啮齿类
7	P. gallinaceum	8A	PGAL8A_00383800	鸟类
8	P. gaboni	SY75	PGSY75_1007700t31	非人灵长类，黑猩猩为主
9	P. ovalecurtisi	GH01	PocGH01_08015600	人类
10	P. ovale wallikeri	CR01	PowCR01_080012800	人类
11	P. praefalciparum	G01	PPRFG01_1008900	非人灵长类，大猩猩为主
12	P. reichenowi	CDC	PRCDC_1007100	非人灵长类，黑猩猩为主
13	P. relictum	SGS1	PRELSG_0805400	鸟类
14	P. vivaxlike	Pvl01	PVL_080012000t42	非人灵长类
15	P. vivax	P01	PVP01_0807400	人类
16	P. vinckei	CY	PVVCY_1200670	啮齿类