Haploid-resolved genome assemblies for the arboviral vectors Aedes aegypti and Aedes mascarensis

虫媒病毒载体埃及伊蚊和马斯卡伊蚊的单倍体解析基因组组装

• 批准号: 10495269
• 负责人: IGOR V SHARAKHOV
• 金额: $ 19.53万
• 依托单位: VIRGINIA POLYTECHNIC INST AND ST UNIV
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-24 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10495269
• 关键词: Address; Aedes; Aedes aegypti genome; Anopheles Genus; Arbovirus Infections; Arboviruses; Backcrossings; COVID-19; Chikungunya virus; Chromosome 1; Chromosomes; Communities; Culicidae; Cytogenetics; Dengue; Dengue Fever; Dengue Virus; Development; Disease Outbreaks; Disease Vectors; Epidemic; Eye; Female; Fluorescent in Situ Hybridization; Genes; Genetic; Genetic Recombination; Genome; Genomic Segment; Genomics; Goals; Haploidy; Haplotypes; Hi-C; Human; Hybrids; Individual; Insecticide Resistance; Intersex; Knowledge; Laboratories; Latin America; Link; Maps; Methods; Minor Lymphocyte Stimulatory Loci; Mosaicism; Mosquito Control; Mosquito-borne infectious disease; Permeability; Phase; Phenotype; Physical Chromosome Mapping; Population; Prevention; Research; Research Personnel; Resolution; Resources; Risk; Technology; Time; Transgenic Organisms; Translating; Variant; Vector-transmitted infectious disease; Vectorial capacity; Yellow Fever; Zika Virus; base; chromosome conformation capture; contig; cost effective; disorder control; improved; innovation; male; nanopore; novel; physical mapping; prevent; reference genome; reproductive; scaffold; sex; single molecule; tool; vector; vector control; zika fever

Haploid-resolved genome assemblies for the arboviral vectors Aedes aegypti and Aedes mascarensis Project Summary/Abstract Aedes aegypti transmits several arboviral diseases including dengue and Zika fever, which threaten half of the human population worldwide. In this study, we will take advantage of Oxford Nanopore Technology (ONT) sequencing, the TrioCanu binning approach, and Hi-C scaffolding to create haploid-resolved chromosome- level genome assemblies for Ae. aegypti and Ae. mascarensis. These two closely related species show reproductive isolation by hybrid breakdown via formation of intersexes in backcross hybrids. The long-term objective of this research is to decipher the genetic mechanisms of reproductive isolation between Ae. aegypti and closely related species and to translate such fundamental knowledge into safe and efficient methods to control mosquito-borne infectious diseases. Understanding the permeability of species boundaries is increasingly urgent because of recent developments in transgenic- and gene drive-based applications to control disease vectors. The major goal of this proposed R21 project is to develop and validate phased or haplotype-resolved genome assemblies for Ae. aegypti and Ae. mascarensis and use them for identification and characterization of the genomic regions associated with intersex phenotypes in backcross hybrids between the two species. This timely project will meet the demand for new, highly-finished genome references for arboviral vectors based on appropriate innovative tools and the PI’s and Co-I’s expertise. Toward this goal, we propose the following three Specific Aims: (1) Obtain contiguous haploid genome assemblies for the Ae. aegypti RED strain and Ae. mascarensis by integrating ONT, Illumina sequencing, trio binning, and chromosome-scale Hi-C scaffolding; (2) Validate the obtained assemblies and construct high-resolution physical genome maps for Ae. aegypti and Ae. mascarensis using fluorescence in situ hybridization (FISH); and (3) Identify genomic regions in chromosome 1 that are associated with intersex phenotypes. The new, haploid-resolved chromosome-level genome assemblies for Ae. aegypti and Ae. mascarensis will be available to the scientific community through VEuPathDB and NCBI. Identification of the recombination breakpoints and characterization of genomic regions associated with intersex phenotypes will improve our understanding of the mechanisms that maintain species boundaries and determine sex in mosquitoes. The project will also help us to detect genome variations between these two species that may be important for speciation, adaptation, and vectoral capacity.

单倍体分辨的基因组组件，用于Arboviral Vectors Aedes aegypti和Aedes Mascarensis 项目摘要/摘要 埃及埃及传播了包括登革热和寨卡病毒在内的几种arboviral疾病，威胁到一半 全球人口。在这项研究中，我们将利用牛津纳米孔技术（ONT） 测序，三核binning方法和Hi-C脚手架，以创建单倍体分辨的染色体 - AE的水平基因组组件。埃及和ae。睫毛膏。这两个密切相关的物种显示 通过杂交分解，通过形成杂交杂种中的杂种分解。长期 这项研究的目的是破译AE之间生殖隔离的遗传机制。埃及 和密切相关的物种，并将这种基本知识转化为安全有效的方法 控制蚊子传染病。了解物种边界的渗透性是 由于最新的转基因和基因驱动器应用程序的发展，越来越紧迫 控制疾病向量。该拟议的R21项目的主要目标是开发和验证分阶段或 AE的单倍型分辨基因组组件。埃及和ae。 Mascarensis并将其用于识别 和反向杂交中与中性表型相关的基因组区域的表征 在两个物种之间。这个及时的项目将满足对新的，高级基因组参考的需求 用于基于适当的创新工具以及PI和Co-I的专业知识的Arboviral载体。达到这个目标， 我们提出以下三个特定目标：（1）获得AE的连续单倍体基因组组件。 埃及红菌株和AE。通过整合ONT，Illumina测序，三重奏组和 染色体规模的Hi-C脚手架； （2）验证获得的组件并构建高分辨率 AE的物理基因组图。埃及和ae。使用荧光原位杂交（FISH）使用荧光； （3）确定与中性表型相关的染色体1中的基因组区域。新的， 单倍体分辨的染色体级基因组组件的AE。埃及和ae。睫毛膏可用 通过VeupathDB和NCBI向科学界。重组断点的识别和 与中性表型相关的基因组区域的表征将提高我们对 维持物种边界并确定蚊子中性别的机制。该项目也将帮助我们 检测这两个物种之间的基因组变异，这些变异对于规范，适应和 矢量能力。