A New Foundation for Leishmaniasis Vector Research and Control Through Generation of High-quality Sand Fly Genome Assemblies.

通过生成高质量沙蝇基因组组合为利什曼病媒介研究和控制奠定新基础。

• 批准号: 10043436
• 负责人: MARY A MCDOWELL
• 金额: $ 9.25万
• 依托单位: UNIVERSITY OF CALIFORNIA AT DAVIS
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-10 至 2021-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10043436
• 关键词: Adult; Alternative Splicing; American; Biological Sciences; Biology; Blood; CRISPR/Cas technology; Chromatin; Chromosome Positioning; Chromosomes; Complex; Computer software; Culicidae; Cutaneous Leishmaniasis; DNA Sequence; DNA sequencing; Data; Data Set; Dengue; Deposition; Development; Disease; Disease Vectors; Effectiveness; Environment; Female; Foundations; Future; Genbank; Generations; Genes; Genome; Genomics; Haploidy; Haplotypes; Human; Human Bites; Incidence; India; Individual; Leishmania; Leishmaniasis; Libraries; Life; Lutzomyia genus; Malaria; Medical; Methods; Middle East; Monitor; Morbidity - disease rate; Northern Africa; Optics; Parasites; Phlebotomus; Population; Population Sizes; Prevention Research; Procedures; Production; Publications; Reproduction; Research; Resources; Sand Flies; Sex Chromosomes; Software Validation; Structure; Techniques; Technology; Vaccines; Validation; Visceral Leishmaniasis; Wolbachia; base; computing resources; cost; disability-adjusted life years; disorder control; experimental study; gene drive system; genetic analysis; genome annotation; genome-wide; gut microbiota; improved; instrument; interest; male; microbiome; microbiome components; microbiome sequencing; mortality; new technology; pesticide resistance; prevent; reference genome; resistance allele; scaffold; sequencing platform; sex; transcriptome; transcriptome sequencing; transmission process; transmission-blocking vaccine; vector; vector control; vertebrate genome

Project Summary Leishmaniasis is the second biggest parasitic killer after malaria. It is estimated to kill an estimated 40,000 people every year, and accounts for an estimated 2.4 million disability-adjusted life-years (DALYs). The Leishmania parasite is transmitted to humans when female sand flies bite humans to obtain blood meals that they require for reproduction. A better understanding of sand fly biology and populations is important for the control and monitoring of this disease vector. This proposal will generate a high-quality genome references to support future sand fly and Leishmania control efforts. New and ongoing methods of integrated vector control are improved by genomic analysis. Descriptions of species complexes, estimation of effective population sizes, monitoring of pesticide resistance allele emergence, and assessment of changes in population structure can all be accomplished using genetic analyses. New vector control methods based on CRISPR-Cas9 manipulation to create gene drives to prevent transmitting malaria and microbiome manipulation with Wolbachia to prevent transmission of dengue are being trialed in mosquitoes. Unfortunately, our early attempts to create high-quality genome reference resources for sand flies were not successful. This study will generate new, very high-quality reference genome sequences for two critical sand fly species: Lutzomyia longipalpis, found in the New World, is the primary vector of American visceral leishmaniasis and Phlebotomus papatasi, found in the Old World, including northern Africa, the Middle East and India, is a vector of cutaneous leishmaniasis. New DNA sequencing and genome assembly techniques have improved the quality and reduced the cost to generate new reference genomes. This study will generate multiple high-quality DNA sequence information datasets for new high-quality genome assemblies. The primary sequence information will be long read (10-15 thousand bases) high accuracy (> 99.8%) DNA sequences using new DNA sequencing platforms from a single individual of each species. HiC chromatin sequence data will be generated to understand the relative chromosome position of the sequences. Optical mapping data will enable better scaffolding and validation of the final assembly. A genome assembly software pipeline based on the vertebrate genome assembly pipeline currently generating the highest quality reference genome assemblies will be used to assemble the data as much as possible separating haplotypes. Long read high accuracy transcriptome data will be generated to support a high-quality genome annotation, and the sand flies' microbiomes to fully characterize the environment of Leishmania in these vectors. The final product will be a high-quality genome reference foundation for future efforts to monitor and control the vector of this devastating disease.

项目摘要 利什曼病是仅次于疟疾的第二大寄生虫杀手。据估计，它造成约4万人死亡 每年，估计有240万个伤残调整生命年。利什马尼亚 当雌性沙蝇叮咬人类以获取它们所需的血液时，寄生虫就会传播给人类。 用于繁殖。更好地了解沙蝇的生物学和种群对于控制和 对这种病媒的监测。这项建议将生成高质量的基因组参考文献，以支持未来 沙蝇和利什曼病的控制努力。 新的和正在进行的综合病媒控制方法通过基因组分析得到改进。描述： 物种复合体，有效种群大小的估计，农药抗性等位基因出现的监测， 对种群结构变化的评估都可以使用遗传分析来完成。新载体 基于CRISPR-Cas9操纵的控制方法，以创建基因驱动以防止疟疾传播和 利用沃尔巴克氏菌进行微生物群操作以防止登革热传播的试验正在蚊子身上进行。 不幸的是，我们早期试图为沙蝇创造高质量的基因组参考资源的努力没有成功 成功。这项研究将为两个关键的沙蝇产生新的、非常高质量的参考基因组序列 种类：美洲内脏利什曼病的主要传播媒介是新大陆发现的Lutzmyia long gipalpis 和白头翁，发现于东半球，包括北非，中东和印度，是一种 皮肤利什曼病病媒。 新的DNA测序和基因组组装技术提高了质量，降低了成本 产生新的参考基因组。这项研究将产生多种高质量的DNA序列信息 用于新的高质量基因组组件的数据集。将长时间读取初级序列信息(10-15 千碱基)高准确率(&gt；99.8%)使用新的DNA测序平台 每一物种的个体。将生成的HIC染色质序列数据理解为 序列的染色体位置。光学映射数据将使更好的脚手架和验证 总装。一种基于脊椎动物基因组组装流水线的基因组组装软件流水线 目前，生成最高质量的参考基因组组合将被用来收集尽可能多的数据 尽可能分离单倍型。将生成长读高精度转录组数据，以支持 高质量的基因组注释，以及沙蝇的微生物群，以充分描述 这些媒介中的利什曼原虫。最终产品将成为未来高质量的基因组参考基础 努力监测和控制这种毁灭性疾病的病媒。