利用选择性全基因组扩增（SWGA）方法，从被忽视的疟原虫间日疟原虫和卵形疟原虫中获取基因组见解。

Leveraging genomic insights from the neglected malaria parasites P. malariae and P. ovale using selective whole genome amplification (SWGA) approach.

作者信息

Ben-Rached Fathia, Subudhi Amit Kumar, Li Chang, Alawi Mariah, Satyam Rohit, Xu Sui, Zhu Guoding, Naeem Raeece, Mfarrej Sara, Liu Di, Stead Zenaida, Askonas Caroline, Liu Yaobao, Cao Jun, Pain Arnab

机构信息

Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Kingdom of Saudi Arabia, Thuwal, 23955-6900, Saudi Arabia.

Jiangsu Provincial Key Laboratory On Parasite and Vector Control Technology, Provincial Medical Key Laboratory, Jiangsu Institute of Parasitic Diseases, National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Wuxi, 214064, Jiangsu, China.

出版信息

BMC Genomics. 2025 Feb 7;26(1):118. doi: 10.1186/s12864-025-11292-8.

DOI:10.1186/s12864-025-11292-8

PMID:39920573

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11804106/

Abstract

BACKGROUND

Systematic genomics-guided population-based studies on the neglected malaria parasites, P. malariae, P. ovale curtisi, and P. ovale wallikeri species remain challenging due to their low parasitemia, underestimation, and lack of comprehensive genetic analysis. Techniques that cost-effectively allow the enriching of the genome of interest from complex genome backgrounds for sequencing studies help immensely to perform genomic analyses. One such technique is selective whole-genome amplification (SWGA).

RESULTS

We applied SWGA using specifically designed primer sets targeting the pathogen genome to enrich parasite DNA from clinical samples. This enabled cost-effective and high-quality WGS for these neglected malaria species. WGS on SWGA-treated samples demonstrated improved genome coverage. Our method outperformed the published protocol for P.malariae with higher enrichment of the targeted genome. On average, P. malariae had 93% of the genome covered by ≥ 10 reads; parallel improvements in genome coverage were achieved for both P. ovale spp. with 81% on average of the genome covered by ≥ 10 reads. Consequently, the detection of thousands of additional SNPs not detectable in pre-SWGA samples was facilitated after SWGA, allowing more substantial downstream population genomics analysis, particularly for the polymorphic and antimalarial genes of great interest for all the species. Furthermore, leveraging the long DNA fragments generated by SWGA, we achieved high-quality genome assemblies for P. malariae and P. ovale using PacBio long reads sequencing technology.

CONCLUSIONS

SWGA approach implemented here provides a powerful tool for enhancing genomic analysis of these neglected parasites, revealing population diversity, drug resistance markers, and hypervariable regions. This methodology constitutes a transformative tool to surmount the challenges of genomic analysis for neglected malaria parasites and can improve malaria research and control.

摘要

背景

由于疟原虫血症水平低、易被低估以及缺乏全面的基因分析，基于系统基因组学的针对被忽视的疟原虫物种——三日疟原虫、卵形疟原虫柯蒂斯亚种和卵形疟原虫瓦利克里亚种的人群研究仍然具有挑战性。能够从复杂基因组背景中经济高效地富集目标基因组以进行测序研究的技术，对开展基因组分析有极大帮助。选择性全基因组扩增（SWGA）就是这样一种技术。

结果

我们使用专门设计的靶向病原体基因组的引物组应用SWGA，从临床样本中富集寄生虫DNA。这使得对这些被忽视的疟原虫物种能够进行经济高效且高质量的全基因组测序（WGS）。对经SWGA处理的样本进行WGS显示基因组覆盖度有所提高。我们的方法优于已发表的三日疟原虫方案，目标基因组的富集程度更高。平均而言，三日疟原虫基因组的93%被≥10条 reads覆盖；卵形疟原虫两个亚种的基因组覆盖度也有类似提升，平均81%的基因组被≥10条 reads覆盖。因此，SWGA后有助于检测出数千个在SWGA前样本中无法检测到的单核苷酸多态性（SNP），从而能够进行更深入的下游群体基因组分析，特别是针对所有物种中极具研究价值的多态性和抗疟基因。此外，利用SWGA产生的长DNA片段，我们使用PacBio长读长测序技术为三日疟原虫和卵形疟原虫实现了高质量的基因组组装。