Oresegun Damilola R, Thorpe Peter, Benavente Ernest Diez, Campino Susana, Muh Fauzi, Moon Robert William, Clark Taane Gregory, Cox-Singh Janet
Division of Infection and Global Health, School of Medicine, University of St Andrews, Scotland, United Kingdom.
Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom.
Front Genet. 2022 May 23;13:855052. doi: 10.3389/fgene.2022.855052. eCollection 2022.
, a malaria parasite of Old World macaque monkeys, is used extensively to model biology. Recently, was found in the human population of Southeast Asia, particularly Malaysia. causes uncomplicated to severe and fatal malaria in the human host with features in common with the more prevalent and virulent malaria caused by . As such, presents a unique opportunity to develop experimental translational model systems for malaria pathophysiology informed by clinical data from same-species human infections. Experimental lines of represent well-characterized genetically stable parasites, and to maximize their utility as a backdrop for understanding malaria pathophysiology, genetically diverse contemporary clinical isolates, essentially wild-type, require comparable characterization. The Oxford Nanopore PCR-free long-read sequencing platform was used to sequence and assemble genomes from frozen clinical samples. The sequencing platform and assembly pipelines were designed to facilitate capturing data and describing, for the first time, () and () multiple gene families in parasites acquired from nature. The gene family members code for antigenically variant proteins analogous to the virulence-associated erythrocyte membrane protein () multiple gene family. Evidence presented here suggests that the family members have arisen through a process of gene duplication, selection pressure, and variation. Highly evolving genes including family members tend to be restricted to relatively unstable sub-telomeric regions that drive change with core genes protected in genetically stable intrachromosomal locations. The comparable and gene family members are counter-intuitively located across chromosomes. Here, we demonstrate that, in contrast to conserved core genes, and genes occupy otherwise gene-sparse chromosomal locations that accommodate rapid evolution and change. The novel methods presented here offer the malaria research community not only new tools to generate comprehensive genome sequence data from small clinical samples but also new insight into the complexity of clinically important real-world parasites.
食蟹猴疟原虫是旧大陆猕猴的一种疟原虫，被广泛用于疟原虫生物学建模。最近，在东南亚人群中发现了食蟹猴疟原虫，尤其是在马来西亚。食蟹猴疟原虫在人类宿主中可引起从无并发症到严重及致命的疟疾，其特征与由恶性疟原虫引起的更普遍且毒性更强的疟疾有共同之处。因此，食蟹猴疟原虫为开发基于同物种人类感染临床数据的疟疾病理生理学实验性转化模型系统提供了独特机会。食蟹猴疟原虫的实验株代表了特征明确的基因稳定寄生虫，为了最大限度地发挥其作为理解疟疾病理生理学背景的效用，需要对基因多样的当代临床分离株（本质上是野生型）进行类似的表征。牛津纳米孔无PCR长读长测序平台用于对冷冻临床样本中的食蟹猴疟原虫基因组进行测序和组装。该测序平台和组装流程旨在便于首次捕获数据并描述从自然界获取的寄生虫中的var（可变抗原）和rif（富含精氨酸的膜蛋白）多个基因家族。var基因家族成员编码与毒力相关的红细胞膜蛋白1（PfEMP1）多个基因家族类似的抗原变异蛋白。此处提供的证据表明，var家族成员是通过基因复制、选择压力和变异过程产生的。包括var家族成员在内的高度进化基因往往局限于相对不稳定的亚端粒区域，这些区域推动变化，而核心基因则在基因稳定的染色体内位置受到保护。相比之下，rif和var基因家族成员在染色体上的定位出人意料。在这里，我们证明，与保守的核心基因不同，rif和var基因占据了其他基因稀少的染色体位置，这些位置能够适应快速进化和变化。本文介绍的新方法不仅为疟疾研究界提供了从小临床样本生成全面基因组序列数据的新工具，还为临床上重要的现实世界寄生虫的复杂性提供了新见解。
