Single-cell functional and population genomic analysis of Plasmodium knowlesi malaria parasites

诺氏疟原虫疟原虫的单细胞功能和群体基因组分析

• 批准号: 1618502
• 金额: --
• 依托单位: London School of Hygiene & Tropical Medicine
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-1618502
• 关键词: Single; cell; functional; population; genomic

Strategic Research Priority: Bioscience for HealthAbstract Genomic analyses of parasites can give insights into mechanisms of adaptation to different hosts. There are divergent genetic types of Plasmodium knowlesi infecting humans, now discovered to be associated with different macaque monkey reservoir host species. Sequence analysis reveals substantial genome-wide divergence between these types, although this is particularly high in some chromosomal regions. Analysis of P. knowlesi will be undertaken by flow cytometric sorting from blood of macaque and human fresh isolates, and results of sequence analyses will enable design of genetic manipulation experiments to test for loci that are involved in host adaptation and potentially enhancing reproductive isolation. Project Genomic and functional studies of parasites enable discovery of mechanisms of adaptation to different host species. The zoonotic parasite Plasmodium knowlesi is increasingly commonly seen as a cause of malaria in humans in Southeast Asia, with divergent genetic types (termed Cluster 1 and Cluster 2) now discovered to be predominantly associated with different monkey reservoir host species (long-tailed and pig-tailed macaques respectively). Sequence analysis reveals genome-wide divergence between these types of a level equating to sub-species, although there are chromosomal regions with even higher levels of fixed differences between the types. Many infections contain multiple genotypes, and macaque infections frequently contain additional parasite species. This project will undertake analysis of P. knowlesi by flow cytometric sorting from blood of macaque and human fresh isolates, and sequencing from single cells and pools of individual sorted cells. The analyses of parasites will be from natural macaque as well as human infections, and may potentially also involve analysis of parasites from infected mosquitoes to test a hypothesis of vector-specific susceptibility to the divergent P. knowlesi types. Samples of human infections will be selected to include : (a) Cluster 1 type parasites, (b) Cluster 2 type parasites, and (c) putatively mixed type infections. Samples from macaques will be separately chosen that have either Cluster 1 or Cluster 2 parasites - these will be the first full genome sequences attempted from wild macaque parasites. The 'H strain' parasite long maintained in rhesus macaques has been adapted for growth in human erythrocytes - this is divergent from both cluster 1 and cluster 2 parasites and will be used for allelic replacement studies. Techniques: Flow cytometric sorting and cloning of parasites; Genome sequencing; Transcriptome analysis; Genetic manipulation of parasites; Bioinformatic analyses of gene structure and function

战略研究重点：摘要寄生虫的基因组分析可以深入了解适应不同宿主的机制。感染人类的诺氏疟原虫有不同的遗传类型，现在发现与不同的猕猴宿主物种有关。序列分析揭示了这些类型之间的大量基因组范围的差异，尽管这在某些染色体区域特别高。 将通过从猕猴和人类新鲜分离株的血液中进行流式细胞术分选来分析诺氏疟原虫，序列分析的结果将能够设计遗传操作实验，以检测参与宿主适应和潜在增强生殖隔离的基因座。寄生虫的基因组和功能研究有助于发现适应不同宿主物种的机制。人畜共患寄生虫诺氏疟原虫（Plasmodium knowlesi）越来越常被视为东南亚人类疟疾的原因，目前发现不同的遗传类型（称为聚类1和聚类2）主要与不同的猴子宿主物种（分别为长尾和猪尾猕猴）有关。序列分析揭示了这些类型之间的全基因组差异，其水平相当于亚种，尽管在这些类型之间存在具有更高水平的固定差异的染色体区域。许多感染包含多种基因型，猕猴感染经常包含其他寄生虫物种。该项目将通过从猕猴和人类新鲜分离物的血液中进行流式细胞术分选，并从单个细胞和单个分选细胞池中进行测序来分析诺氏疟原虫。寄生虫的分析将来自天然猕猴以及人类感染，并且可能还涉及来自受感染蚊子的寄生虫的分析，以测试对不同诺氏疟原虫类型的媒介特异性易感性的假设。将选择人类感染样本，包括：（a）簇1型寄生虫，（B）簇2型寄生虫，和（c）脓疱混合型感染。将分别选择具有簇1或簇2寄生虫的猕猴样本-这些将是首次尝试从野生猕猴寄生虫中获得全基因组序列。长期维持在恒河猴中的“H株”寄生虫已适应于在人类红细胞中生长-这与第1簇和第2簇寄生虫不同，并将用于等位基因替代研究。技术：寄生虫的流式细胞仪分选和克隆;基因组测序;转录组分析;寄生虫的基因操作;基因结构和功能的生物信息学分析