Chromosome-based genome assembly for Culex quinquefasciatus

基于染色体的致倦库蚊基因组组装

• 批准号: 8511874
• 负责人: Maria Sharakhova
• 金额: $ 25.14万
• 依托单位: VIRGINIA POLYTECHNIC INST AND ST UNIV
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-01-15 至 2014-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8511874
• 关键词: Advanced Development; Aedes; Anopheles Genus; Anopheles gambiae; Biology; Chromosome Band; Chromosome Structures; Chromosomes; Chromosomes, Human, Pair 16; Communicable Diseases; Confusion; Culex (Genus); Culicidae; Cytogenetic Map; Drosophila genus; Encephalitis Viruses; Evolution; Filarial Elephantiases; Fluorescent in Situ Hybridization; Genes; Genetic Variation; Genome; Genome Mappings; Genomics; Goals; Grant; Haplotypes; Housing; Human; Larva; Lead; Mammals; Maps; Mitotic; Mitotic Chromosome; Mosquito-borne infectious disease; Preparation; Public Health; Research; Resolution; Risk; Sequence Alignment; Social Welfare; Taxon; Techniques; Technology; United States National Institutes of Health; West Nile virus; base; comparative genomics; genome sequencing; imaginal disc; improved; insight; next generation; next generation sequencing; paralogous gene; pathogen; physical mapping; public health relevance; vector; vector control; vector mosquito

DESCRIPTION (provided by applicant): Mosquitoes are vectors of numerous infectious diseases. To facilitate the development of advanced genome-based strategies for vector control, the genomes of the three major mosquito genera-Anopheles, Aedes, and Culex-were sequenced over the last decade. The genome assembly of Cx. quinquefasciatus, the major vector of the lymphatic filariasis worm and encephalitis viruses, is the most fragmented, with only 9% of the genome placed to the chromosomes. The lack of a high-quality, chromosome-based genome assembly for Cx. quinquefasciatus remains an impediment to further progress in Culex biology and comparative genomics of mosquitoes. Using the Next-Generation Focus Genome Sequencing (FGS) approach, recently developed by Amplicon Express, we will obtain ~250 Mb of high-quality sequence assemblies for 2304 BAC clones. Alignment of the sequences to the existing genome will greatly enhance the quality of the genome assembly. The total number of supercontigs will be reduced from 3171 to ~600. In addition, our project will develop a new cytogenetic map for Cx. quinquefasciatus based on mitotic chromosomes from imaginal discs of 4th instar larvae and anchor the majority of the genomic supercontigs to this map. The primary goal of this R21 proposal is to significantly improve the genome assembly for Cx. quinquefasciatus. The specific aims for this project are to: 1) improve the quality of the genome assembly by sequencing 2304 BAC clones using Focus Genome Sequencing (FGS) and 2) create a chromosome-based genome assembly by multicolor fluorescent in situ hybridization (FISH) of ~1000 BAC clones to Cx. quinquefasciatus chromosomes. The availability of a high-quality genome assembly for Cx. quinquefasciatus will enhance research in vector biology. Results of this project will be disseminated through VectorBase.

描述（由申请人提供）：蚊子是多种传染病的媒介。为了促进基于基因组的先进病媒控制策略的开发，在过去十年中对三大蚊属——按蚊、伊蚊和库蚊——的基因组进行了测序。 Cx 的基因组组装。致死五线虫是淋巴丝虫病和脑炎病毒的主要载体，其片段化程度最高，只有 9% 的基因组位于染色体上。缺乏高质量、基于染色体的 Cx 基因组组装。致倦库蚊仍然是库蚊生物学和蚊子比较基因组学进一步进展的障碍。使用 Amplicon Express 最近开发的下一代焦点基因组测序 (FGS) 方法，我们将为 2304 个 BAC 克隆获得约 250 Mb 的高质量序列组件。将序列与现有基因组进行比对将大大提高基因组组装的质量。超级重叠群的总数将从 3171 个减少到约 600 个。此外，我们的项目将为 Cx 开发新的细胞遗传学图谱。 quinquefasciatus 基于来自 4 龄幼虫成虫盘的有丝分裂染色体，并将大部分基因组超重叠群锚定到该图谱上。 R21 提案的主要目标是显着改进 Cx 的基因组组装。致倦五线虫。该项目的具体目标是：1) 通过使用焦点基因组测序 (FGS) 对 2304 个 BAC 克隆进行测序来提高基因组组装的质量，2) 通过约 1000 个 BAC 克隆与 Cx 的多色荧光原位杂交 (FISH) 创建基于染色体的基因组组装。致倦昆奎染色体。高质量 Cx 基因组组装的可用性。 quinquefasciatus 将加强媒介生物学的研究。该项目的成果将通过 VectorBase 传播。