Characterizing the Pan-genome of a Rickettsia Infecting the Eastern Black-legged Tick

感染东部黑腿蜱的立克次体的全基因组特征

• 批准号: 10115952
• 负责人: Timothy P Driscoll
• 金额: $ 24.38万
• 依托单位: UNIVERSITY OF MARYLAND BALTIMORE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-22 至 2022-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10115952
• 关键词: Abbreviations; Address; Adult; Alleles; Anaplasma phagocytophilum; Anaplasmosis; Antibiotics; Area; Arthropods; Babesia; Babesiosis; Bacteria; Biology; Biotin; Black-legged Tick; Borrelia; Cell Line; Cells; Characteristics; Chromosomes; Communicable Diseases; Data; Deer Tick; Disease; Disease Vectors; Distant; Elements; Evaluation; Flavivirus; Frequencies; Future; Gene Expression; Genes; Genetic Variation; Genome; Genomics; Geography; Goals; Health; Horizontal Gene Transfer; Human; Infection; Inherited; Life Style; Lyme Disease; Maintenance; Mediating; Metabolic; Microbe; Mobile Genetic Elements; Names; Nature; Nutrient; Nymph; Parasites; Pathogenesis; Pathogenicity; Peptide Synthesis; Population; Powassan virus; Prevalence; Process; Proteins; Pseudogenes; Research; Resistance; Resolution; Resources; Rickettsia; Rickettsia rickettsii; Rocky Mountain Spotted Fever; Role; STEM research; Shapes; Specialist; Testing; Theileria; Theileriasis; Tick-Borne Diseases; Ticks; United States; Vertebrates; Work; combat; contig; deep sequencing; design; endosymbiont; experimental study; feeding; genetic element; genetic variant; genomic variation; host microbiota; human disease; human pathogen; infection rate; innovation; insight; microbial; novel; pan-genome; parasitism; pathogen; reference genome; reproductive; spreading factor; superinfection; tick population; tick-borne; tool; transcriptome sequencing; vector transmission; vector-borne pathogen

PROJECT SUMMARY Microbial residents of arthropod disease vectors engender profound effects on the biology of their host, both positive (e.g., nutrient acquisition, defense from pathogens) and negative (e.g., reproductive parasitism). The mechanisms that underpin these microbial processes arise as evolutionary consequences of genetic variation and are often mediated by mobile genetic elements (MGEs). Even when these resident microbes are not known to be pathogenic, their impact on host biology can influence the distribution and transmission of vector-borne pathogens. The deer tick, Ixodes scapularis, is widely distributed in the Eastern United States and is an important transmitter of several human pathogens, including Borrelia species (Lyme disease) and Anaplasma phagocytophilum (anaplasmosis). Deer ticks also harbor a prevalent intracellular bacterium, Rickettsia buchneri, that is unique among Rickettsia species in several ways: 1) it is vertically inherited with high efficiency in the deer tick, but does not cycle between ticks and vertebrates in nature; 2) it is, astonishingly, the only Rickettsia species that has ever been detected in I. scapularis; and 3) its genome is substantially enriched with pseudogenes and MGEs that carry intriguing cargo, including genes for biotin synthesis, antibiotic synthesis and resistance, and nonribosomal peptide synthesis. Given its maintenance in deer ticks, and its arsenal of potential functions, R. buchneri stands to exert significant influence on the biology of this important disease vector. The long-term goal of this research is to determine the nature of the relationship between R. buchneri and I. scapularis. The current work is designed to advance this research goal by addressing significant challenges; namely, the lack of a high-quality reference genome, inconsistencies in infection rate and distribution data, and a dearth of information regarding strain-level genomic variation. The central hypothesis of this project is that high-resolution data on infection rate and genomic population substructure will elucidate R. buchneri's trajectory toward an obligate endosymbiotic lifestyle. The proposed work will gauge the extent of species-specific innovation in R. buchneri by using 1) long-read sequencing to generate a closed genome, 2) RNA-seq to confirm pseudogene prediction, and 3) phylogenomics to characterize genes and other genomic elements unique to R. buchneri (AIM 1). The current proposal work will also characterize the R. buchneri pan-genome by using 1) quantitative PCR to assess its infection rate among natural populations of deer ticks, 2) short-read deep sequencing to determine the distribution of R. buchneri genetic variants, alleles, and MGEs, and 3) phylogenomics to characterize the extent (and origin) of lateral gene transfers into R. buchneri (AIM 2). Illuminating R. buchneri genomic variation and tick infection frequency will lead to insights into its relationship with the deer tick and ultimately inform future efforts to use its repertoire of MGEs as gene drive tools for spreading factors to combat tick-borne diseases.

项目摘要 节肢动物疾病载体的微生物居民对宿主的生物学产生深远影响 阳性（例如，养分，病原体的防御）和阴性（例如生殖寄生虫）。这 支撑这些微生物过程的机制是遗传变异和 通常是由移动遗传因素（MGE）介导的。即使这些居民微生物不知道 致病性，它们对宿主生物学的影响会影响载体传播病原体的分布和传播。 鹿tick t，ixodes capularis，广泛分布在美国东部，是 几种人类病原体，包括疏葡萄虫（莱姆病）和吞噬细胞吞噬细胞。 （肿瘤病）。鹿tick虫还带有一个普遍的细胞内细菌，即立克西亚buchneri，这是独一无二的 立克物种在几种方面：1）垂直遗传在鹿的壁虱中效率高，但不会循环 在自然界中的壁虱和脊椎动物之间； 2）令人惊讶的是，这是唯一被检测到的立克人物 在肩cap骨中； 3）它的基因组大大富含富含货物的伪基和MGE， 包括生物素合成，抗生素合成和抗性以及非核糖体肽合成的基因。给出 R. Buchneri在鹿壁虱中的维护及其潜在功能的武器 关于这个重要疾病载体的生物学。 这项研究的长期目标是确定R. Buchneri和I之间关系的性质。 肩cap骨。当前的工作旨在通过解决重大挑战来促进这一研究目标。即， 缺乏高质量的参考基因组，感染率和分布数据的不一致以及缺乏 有关应变水平基因组变异的信息。该项目的中心假设是高分辨率 关于感染率和基因组种群子结构的数据将阐明R. Buchneri的轨迹 内共生生活方式。拟议的工作将评估R. Buchneri中物种特定创新的程度 使用1）长阅读测序生成封闭的基因组，2）RNA-seq确认伪元预测，3） 系统基因学以表征基因和其他基因组元素（AIM 1）。电流 提案工作还将通过使用1）定量PCR来评估其感染。 鹿tick的天然种群的速率，2）简短阅读的深度测序以确定R的分布。 buchneri遗传变异，等位基因和MGE和3）系统基因学表征侧面的程度（和起源） 基因转移到R. buchneri（AIM 2）中。照明R. buchneri基因组变异和tick感染频率将 导致深入了解其与鹿tick的关系，并最终告知未来的努力，以利用其MGES曲目 作为传播因素以打击tick传播疾病的基因驱动工具。