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

基本信息

批准号：
10352741
负责人：
IGOR V SHARAKHOV
金额：
$ 23.73万
依托单位：
VIRGINIA POLYTECHNIC INST AND ST UNIV
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-09-24 至 2023-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10352741
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

项目摘要

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.

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项目概要/摘要埃及伊蚊传播多种虫媒病毒疾病，包括登革热和寨卡热，这威胁着一半的人口在这项研究中，我们将利用牛津纳米孔技术（ONT）。测序、TrioCanu 分箱方法和 Hi-C 支架来创建单倍体解析的染色体埃及伊蚊和马斯卡伊伊蚊的水平基因组组装。通过回交杂交中形成雌雄同体的杂交破坏进行生殖隔离。本研究的目的是破译埃及伊蚊之间生殖隔离的遗传机制。和密切相关的物种，并将这些基础知识转化为安全有效的方法了解物种边界的渗透性是控制蚊媒传染病的关键。由于最近基于转基因和基因驱动的应用的发展，这一问题变得越来越紧迫该拟议 R21 项目的主要目标是开发和验证分阶段或埃及伊蚊和马斯卡伊蚊的单倍型解析基因组组装并用它们进行鉴定。回交杂交中与双性表型相关的基因组区域的表征这个及时的项目将满足对新的、高度完成的基因组参考的需求。基于适当的创新工具以及 PI 和 Co-I 的专业知识来实现虫媒病毒载体。我们提出以下三个具体目标：（1）获得伊蚊的连续单倍体基因组组装。通过整合 ONT、Illumina 测序、trio binning 和 Ae. mascarensis (2) 验证获得的组装体并构建高分辨率使用荧光原位杂交 (FISH) 绘制埃及伊蚊和马斯卡伊伊蚊的物理基因组图谱； (3) 鉴定 1 号染色体中与双性表型相关的基因组区域。埃及伊蚊和马斯卡伊伊蚊的单倍体解析染色体水平基因组组装将可用。通过 VEuPathDB 和 NCBI 向科学界提供重组断点的鉴定和信息。与双性表型相关的基因组区域的表征将提高我们对双性表型的理解维持物种边界和确定蚊子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，这对于物种形成、适应和进化可能很重要矢量容量。