Genetic polymorphism and interspecific evolution of the PfAP2-I gene coding sequence in Plasmodium falciparum

doi:10.20199/j.issn.1672-2302.2026.03.002

Abstract

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

CLC Number:

R382.3+1

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.

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References 38

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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