Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea.
Malar J. 2018 Mar 14;17(1):115. doi: 10.1186/s12936-018-2256-y.
Human infections due to the monkey malaria parasite Plasmodium knowlesi is on the rise in most Southeast Asian countries specifically Malaysia. The C-terminal 19 kDa domain of PvMSP1P is a potential vaccine candidate, however, no study has been conducted in the orthologous gene of P. knowlesi. This study investigates level of polymorphisms, haplotypes and natural selection of full-length pkmsp1p in clinical samples from Malaysia.
A total of 36 full-length pkmsp1p sequences along with the reference H-strain and 40 C-terminal pkmsp1p sequences from clinical isolates of Malaysia were downloaded from published genomes. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 and MEGA 5.0 software. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (F ) and population structure of parasite was determined using Arlequin v3.5 and STRUCTURE v2.3.4 software.
Comparison of 36 full-length pkmsp1p sequences along with the H-strain identified 339 SNPs (175 non-synonymous and 164 synonymous substitutions). The nucleotide diversity across the full-length gene was low compared to its ortholog pvmsp1p. The nucleotide diversity was higher toward the N-terminal domains (pkmsp1p-83 and 30) compared to the C-terminal domains (pkmsp1p-38, 33 and 19). Phylogenetic analysis of full-length genes identified 2 distinct clusters of P. knowlesi from Malaysian Borneo. The 40 pkmsp1p-19 sequences showed low polymorphisms with 16 polymorphisms leading to 18 haplotypes. In total there were 10 synonymous and 6 non-synonymous substitutions and 12 cysteine residues were intact within the two EGF domains. Evidence of strong purifying selection was observed within the full-length sequences as well in all the domains. Shared haplotypes of 40 pkmsp1p-19 were identified within Malaysian Borneo haplotypes.
This study is the first to report on the genetic diversity and natural selection of pkmsp1p. A low level of genetic diversity and strong evidence of negative selection was detected and observed in all the domains of pkmsp1p of P. knowlesi indicating functional constrains. Shared haplotypes were identified within pkmsp1p-19 highlighting further evaluation using larger number of clinical samples from Malaysia.
在大多数东南亚国家，尤其是马来西亚，由于猴疟原虫感染人体导致的疟疾病例呈上升趋势。PvMSP1P 的 C 端 19 kDa 结构域是一种潜在的疫苗候选物，但尚未在 P. knowlesi 的同源基因中进行研究。本研究调查了马来西亚临床样本中全长 pkmsp1p 的多态性、单倍型和自然选择水平。
从已发表的基因组中下载了 36 条全长 pkmsp1p 序列以及参考 H 株和 40 条来自马来西亚临床分离株的 C 端 pkmsp1p 序列。使用 DnaSP 5.10 和 MEGA 5.0 软件确定遗传多样性、多态性、单倍型和自然选择。使用 NETWORK 软件 v5.0 中的单倍型网络树确定系统发育关系。使用 Arlequin v3.5 和 STRUCTURE v2.3.4 软件确定种群遗传分化指数（Fst）和寄生虫的种群结构。
比较 36 条全长 pkmsp1p 序列与 H 株，共发现 339 个 SNP（175 个非同义突变和 164 个同义突变）。全长基因的核苷酸多样性与其同源基因 pvmsp1p 相比较低。与 C 端结构域（pkmsp1p-38、33 和 19）相比，N 端结构域（pkmsp1p-83 和 30）的核苷酸多样性更高。全长基因的系统发育分析确定了来自马来西亚婆罗洲的 2 个不同的 P. knowlesi 簇。40 条 pkmsp1p-19 序列显示出较低的多态性，其中 16 个多态性导致 18 个单倍型。共有 10 个同义突变和 6 个非同义突变，两个 EGF 结构域内有 12 个半胱氨酸残基完整。全长序列以及所有结构域都观察到强烈的纯化选择证据。在马来西亚婆罗洲的单倍型内发现了 40 个 pkmsp1p-19 的共有单倍型。
本研究首次报告了 pkmsp1p 的遗传多样性和自然选择。在 P. knowlesi 的 pkmsp1p 的所有结构域中均检测到并观察到遗传多样性水平低和强烈的负选择证据，表明存在功能限制。在 pkmsp1p-19 中发现了共有单倍型，这突出表明需要使用来自马来西亚的更大数量的临床样本进一步评估。
