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基因组组合 项目摘要/摘要 埃及伊蚊传播几种虫媒病毒疾病，包括登革热和寨卡病毒热，这些疾病威胁到一半的 世界各地的人口。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，以创建单倍体解析的染色体- Ae.水平基因组组装。Aegypti和Ae.睫毛膏。这两个亲缘关系密切的物种表明 在回交杂种中，通过形成中间性而导致的杂种破裂所造成的生殖隔离。长期的 本研究的目的是破译Ae之间生殖隔离的遗传机制。埃及伊蚊 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 越来越迫切，因为转基因和基于基因驱动的应用程序最近的发展 控制病媒生物。此提议的R21项目的主要目标是开发和验证阶段性或 Ae.单倍型解析的基因组组件。Aegypti和Ae.并用它们来鉴定 以及与回交杂交种的间性表型相关的基因组区域的特征 在这两个物种之间。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的专业知识的机载病毒载体。为了实现这个目标， 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合。 埃及红菌株和Ae.通过集成ONT、Illumina测序、Trio Bin和 染色体尺度的Hi-C支架；(2)验证获得的组件并构建高分辨率 Ae.的物理基因组图谱Aegypti和Ae.用荧光原位杂交技术(FISH)检测睫毛虫； 以及(3)确定1号染色体上与中间性表型相关的基因组区域。新的， Ae.单倍体分辨的染色体水平基因组组装。Aegypti和Ae.将提供睫毛膏 通过VEuPathDB和NCBI向科学界提供。重组断点的识别和 描述与两性表型相关的基因组区域将有助于我们更好地理解 维持蚊子物种边界和决定性别的机制。该项目也将帮助我们 为了检测这两个物种之间的基因组差异，这些差异可能对物种形成、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.