Highly finished chromosome-based genome assembly for Anopheles gambiae

描述（由申请人提供）：非洲疟疾蚊冈比亚按蚊，由于其在流行病学上的重要性，是第一个被测序的病媒。为了对An进行全基因组注释。冈比亚，所有在这种疟疾媒介中具有生物学作用的序列都必须确定。然而，较大的缺口、部分支架定向错误以及未定位的序列仍然给基因组的准确注释和功能表征带来严重的问题。如果不了解这些缺失序列的内容，对蚊子基因、调控元件和重复元件的完整了解是不完整的。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序列导致了同源基因和来自不同次倍型的基因的混淆。基因贫乏、重复序列丰富的异染色质区域的组装尤其分散，没有发现来自异染色质Y染色体的基因。可读多烯染色体的存在和疟疾对公共卫生的重大影响使安。冈比亚是第一载体，基因组组装高度完成。本R21项目的主要任务是开发高质量的基因组组合，并利用高通量技术探索冈比亚按蚊s型异染色质和Y染色体的遗传含量。自动化原位杂交、下一代测序、激光显微解剖和共聚焦显微分析设备的可用性，以及PI和Co-PI在细胞遗传学和基因组学方面的专业知识，将确保项目目标的成功实现。简而言之，该项目的具体目标是1。通过高通量全基因组重测序和靶向测序BAC/fosmid克隆关闭s型组装中的支架间隙。2. 物理定位和定向测序支架到多染色体。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的An基因组碎片化组装。冈比亚按蚊的萨利。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。Y染色体基因的可用性将允许研究人员开发特定性别的病媒控制干预措施，并进行An的系统发育分析。冈比亚复合体，无渗透并发症。科学界将能够从VectorBase访问新的组装，以进一步挖掘和功能表征An。冈比亚按蚊的基因组。

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.