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达加斯加伊蚊的单倍体分辨基因组组装 项目总结/摘要 埃及伊蚊传播包括登革热和寨卡热在内的几种虫媒病毒疾病， 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、TrioCanu分箱方法和Hi-C支架来创建单倍体分辨的染色体- 水平的基因组组装。aegypti和Ae.马斯卡伦西斯这两个密切相关的物种表明， 通过回交杂种中中间性的形成而导致的杂种分裂的生殖隔离。长期 本研究的目的是揭示Ae. aegypti 和密切相关的物种，并将这些基本知识转化为安全和有效的方法， 控制蚊媒传染病。理解物种边界的渗透性是 由于转基因和基因驱动应用的最新发展， 控制病媒。这个拟议的R21项目的主要目标是开发和验证分阶段或 Ae.的单倍型解析基因组组装aegypti和Ae. mascarensis和使用它们来识别 以及回交杂种中与间性表型相关的基因组区域的表征 这两个物种之间。这一及时的项目将满足对新的、高度完善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，为了实现这一目标， 我们提出了以下三个具体目标：（1）获得Ae的连续单倍体基因组组装体。 埃及伊蚊RED株和埃及伊蚊Ae.通过整合ONT、Illumina测序、三重分箱和 染色体尺度Hi-C支架;（2）将获得的组装体进行测序，构建高分辨率的Hi-C支架。 Ae的物理基因组图谱。aegypti和Ae.荧光原位杂交（FISH）检测乳腺癌; 和（3）鉴定1号染色体中与间性表型相关的基因组区域。新的， Ae.的单倍体分辨染色体水平基因组组装aegypti和Ae. Mascarensis将提供 通过VEuPathDB和NCBI提供给科学界。重组断裂点的鉴定和 与间性表型相关的基因组区域的表征将提高我们对 维持物种界限和决定蚊子性别的机制。该项目还将帮助我们 检测这两个物种之间的基因组变异，这些变异可能对物种形成、适应和 向量容量

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.