Highly finished chromosome-based genome assembly for Anopheles gambiae

描述（由申请方提供）：非洲疟疾蚊子冈比亚按蚊由于其流行病学的重要性，是第一个测序的病媒。为了对An.在冈比亚，必须鉴定在这种疟疾媒介中具有生物作用的所有序列。然而，大的差距，不正确的方向，一些支架，和未映射的序列仍然提出了一个严重的问题，准确的注释和功能表征的基因组。如果没有关于这些缺失序列的信息，对蚊子基因、调控元件和重复元件的完整补充的知识是不完整的。此外，在目前的PEST基因组组装中大量错误组装的“杂交”M和S序列导致旁系同源基因和来自不同单倍型的基因之间的混淆。基因贫乏、重复序列丰富的异染色质区域的组装尤其支离破碎，并且没有发现来自异染色质Y染色体的基因。冈比亚是第一个完成基因组组装的载体的最佳选择。 该R21项目的主要目标是开发高质量的基因组组装，并使用高通量技术探索冈比亚按蚊S型异染色质和Y染色体的遗传内容。自动原位杂交、下一代测序、激光显微切割和共聚焦显微镜分析设备的可用性，以及PI和Co-PI在细胞遗传学和基因组学方面的专业知识，将确保成功实现该项目的目标。简单地说，该项目的具体目标是1。通过BAC/fosmid克隆的高通量全基因组重测序和靶向测序来闭合S型组装中的支架间间隙。2.将测序支架物理映射并定向到多线染色体。3.显微解剖、测序和表征An。冈比亚异染色质和Y染色体。 该项目将极大地改善目前An的片段化基因组组装。冈比亚S型。新的基因组组装将使研究人员能够对最完整的测序集进行功能注释，并与其他载体和模式生物进行更全面的比较基因组学研究。来自Y染色体的基因的可用性将使研究人员能够开发性别特异性载体控制干预措施，并对An进行系统发育分析。冈比亚复合体，没有渗入的并发症。科学界将能够访问VectorBase的新组件，以进一步挖掘和功能表征An。冈比亚基因组。 公共卫生相关性：靶向负责载体能力的基因是控制传染病的新方法。非洲疟疾主要媒介冈比亚按蚊的全基因组注释将有助于确定流行病学上重要的目标。为了实现这一目标，拟议的项目将使用高通量技术开发冈比亚按蚊的高质量基因组组装。

DESCRIPTION (provided by applicant): The African malaria mosquito Anopheles gambiae, because of its epidemiological importance, was the first disease vector sequenced. In order to perform full genome annotation for An. gambiae, all sequences that have a biological role in this malaria vector must be identified. However, large gaps, incorrect orientation of some scaffolds, and unmapped sequences still pose a serious problem for accurate annotation and functional characterization of the genome. Knowledge of the full complement of mosquito genes, regulatory elements, and repetitive elements is incomplete without information about what lies in those missing sequences. Moreover, the abundance of incorrectly assembled "hybrid" M and S sequences in the current PEST genome assembly leads to the confusion between paralogous genes and genes from different hyplotypes. The assembly of gene-poor, repeat-rich heterochromatic regions is especially fragmented, and no gene from the heterochromatic Y chromosome has been found. The presence of readable polytene chromosomes and the paramount impact of malaria on public health make An. gambiae the best choice as the first vector with a highly finished genome assembly. The major thrust of this R21 project is to develop a high-quality genome assembly and to explore the genetic content of heterochromatin and the Y chromosome of Anopheles gambiae S-form using high- throughput technologies. The availability of equipment for automated in situ hybridization, next-generation sequencing, laser microdissection, and confocal microscopic analysis, as well as the expertise of the PI and Co-PI in cytogenetics and genomics, will ensure successful achievement of the project's goals. Briefly, the project's specific aims are to 1. Close interscaffold gaps in the S-form assembly by high-throughput whole-genome resequencing and targeted sequencing of BAC/fosmid clones. 2. Physically map and orient sequencing scaffolds to the polytene chromosomes. 3. Microdissect, sequence, and characterize the An. gambiae heterochromatin and Y chromosome. This project will greatly improve the current fragmented genome assembly for the An. gambiae S-form. A new genome assembly will enable researchers to work on functional annotation of the most complete sequencing set and to perform more comprehensive comparative genomics studies with other vectors and model organisms. The availability of genes from the Y chromosome will allow researchers to develop sex- specific vector control interventions and conduct phylogenetic analysis of the An. gambiae complex without complications of introgression. The scientific community will be able to access the new assembly from VectorBase for further mining and functional characterization of the An. gambiae genome. PUBLIC HEALTH RELEVANCE: Targeting genes responsible for vector competence is a novel approach for controlling infectious diseases. A full genome annotation for the major African malaria vector Anopheles gambiae will facilitate identification of the epidemiologically important targets. Toward this goal, the proposed project will develop a high-quality genome assembly for Anopheles gambiae using high-throughput technologies.