A chromosome-level genome assembly for the major African malaria vector Anopheles gambiae

项目摘要/摘要 非洲疟疾蚊子冈比亚按蚊，由于其流行病学的重要性，是第一个 疾病媒介，2002年测得基因组序列。从那时起，害虫菌株组合仍然是唯一的 关于这一主要的非洲疟疾媒介的可用的染色体水平基因组参考。尽管此程序集具有 近20年来一直是疟疾蚊子功能和种群基因组研究的主力， 它现在无法提供尽可能高质量的分析，因为它在现代社会中是惊人的不完美 标准。该组装具有严重的缺陷，如大量未映射的重叠群、测序和 物理间隙，某些支架的顺序和方向不正确，以及存在源自 姊妹种An.猫头鹰。此外，对天牛的害虫品系也进行了研究。冈比亚不再可用，现有的 不能通过额外的排序来验证或改进装配。因此，完整的批注和 对AN的准确的功能描述。冈比亚的基因组不能被执行。此外，缺乏一种 可靠的参考是种群基因组研究的主要障碍，特别是对那些 有结构基因组的变异。长期以来，测序的高昂成本和基因组的绝对困难 组装使蚊子基因组的重大改进变得令人望而却步。一种新颖的长读测序 技术和创新的支架方法现在允许开发从头开始的染色体水平的基因组 质量上乘、价格合理的组件。此外，多线染色体的可用性确保了高- 分辨率基因组图谱在一个。冈比亚亚目。这个R21项目的主要目标是发展一种染色体水平 基因组组装和探索在AN中的结构基因组变异。冈比亚复合体。这来得正是时候 该项目将满足对非洲主要疟疾媒介的新的高度完成的基因组组装的需求 基于国际和平研究所和国际合作组织的适当创新工具和专业知识。简而言之，该项目的具体目标 目的是(1)获得一个连续的基因组组装。冈比亚亚纲利用牛津纳米孔，光管测序， 和染色体尺度的Hi-C支架；(2)验证获得的组装并构建高分辨率的 An.的物理基因组图。冈比亚亚纲的荧光原位杂交；(3)结构特征 An中的基因组变异。冈比亚复合体。一种新的染色体水平的基因组组装。冈比亚亚纲 将改变研究，因为它将允许最完整的功能注释和最详细的种群 疟疾蚊子分析。异染色质序列的更完整的组装将改善我们的 对基因组“暗物质”的理解，并将促进这种疾病媒介的表观基因组学研究。这个 科学界将可以从VEuPathDB和NCBI免费访问新的程序集。

Project Summary/Abstract The African malaria mosquito Anopheles gambiae, because of its epidemiological importance, was the first disease vector, with a genome sequenced in 2002. Since then the PEST strain assembly remains the only available chromosome-level genome reference for this major African malaria vector. Although this assembly has been the workhorse for functional and population genomic studies of malaria mosquitoes for almost two decades, it is now failing to deliver the highest possible quality of the analyses as it is staggeringly imperfect by the modern standards. The assembly has serious deficiencies such as a large portion of unmapped contigs, sequencing and physical gaps, incorrect order and orientation of some scaffolds, and the presence of haplotypes derived from the sister species An. coluzzii. Moreover, the PEST strain of An. gambiae is no longer available and the existing assembly cannot be validated or improved with additional sequencing. As a result, a complete annotation and an accurate functional characterization of the An. gambiae genome cannot be performed. Also, the lack of a reliable reference represents a major impediment to population genomics studies, especially to those dealing with structural genomic variations. For a long time, the high cost of sequencing and the sheer difficulty of genome assembly has made major improvements of the mosquito genome prohibitive. Novel long-read sequencing technologies and innovative scaffolding approaches now allow developing de novo chromosome-level genome assemblies of superior quality at a reasonable cost. Also, the availability of polytene chromosomes ensures high- resolution genome mapping in An. gambiae. The main goal of this R21 project is to develop a chromosome-level genome assembly and to explore the structural genomic variations in the An. gambiae complex. This timely project will meet the demand for a new highly-finished genome assembly for the major African malaria vector based on the appropriate innovative tools and expertise of the PI and Co-I. Briefly, the project’s specific aims are to (1) Obtain a contiguous genome assembly for An. gambiae using Oxford Nanopore, Illumina sequencing, and chromosome-scale Hi-C scaffolding; (2) Validate the obtained assembly and construct a high-resolution physical genome map for An. gambiae using fluorescence in situ hybridization; (3) Characterize structural genomic variations in the An. gambiae complex. A new chromosome-level genome assembly for An. gambiae will transform research as it will allow the most complete functional annotation and the most detailed population analysis of malaria mosquitoes. The more complete assembly of heterochromatic sequences will improve our understanding of the genomic “dark matter” and will stimulate epigenomic studies of this disease vector. The scientific community will have free access to the new assembly from VEuPathDB and NCBI.