Unified Culex assemblies for improved population-level analysis

统一库蚊组件以改进群体水平分析

• 批准号: 9092877
• 负责人: Scott Emrich
• 金额: $ 20.51万
• 依托单位: UNIVERSITY OF NOTRE DAME
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-02-15 至 2018-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9092877
• 关键词: Advanced Development; Aedes; Affect; Algorithms; Anopheles Genus; Base Sequence; Bioinformatics; Biology; Chromosomes; Communicable Diseases; Communities; Computing Methodologies; Culex (Genus); Culicidae; Cytogenetic Map; Cytogenetics; Development; Encephalitis Viruses; Environment; Family; Filarial Elephantiases; Fluorescent in Situ Hybridization; Fostering; Fruit; Funding; Generations; Genetic Polymorphism; Genome; Genomics; Goals; Grant; Housing; Hybrids; Inbreeding; Information Dissemination; Insecticides; Institution; Link; Maps; Methods; Mitotic Chromosome; National Institute of Allergy and Infectious Disease; Optics; Phlebotominae; Ploidies; Population; Public Health; Quantitative Trait Loci; Reading; Research; Residual state; Resources; Risk; Simuliidae; Students; United States National Institutes of Health; Variant; West Nile virus; Work; base; comparative; comparative genomics; experience; human disease; improved; innovation; multidisciplinary; novel; physical mapping; public health relevance; scaffold; training opportunity; trait; vector; vector control; vector mosquito

 DESCRIPTION (provided by applicant): Mosquitoes are vectors of numerous infectious diseases. To foster the development of advanced genome- based strategies for vector control, over thirty species have been sequenced and their genomes made publically available through the NIAID funded Bioinformatics Resource Center (BRC) VectorBase. The genome assembly of Culex quinquefasciatus, the major vector of the lymphatic filariasis worm and encephalitis viruses, however remains the most highly fragmented of the major mosquitoes with only 13% of its genome placed onto chromosomes. The lack of a high-quality, chromosome-based genome assembly for Cx. quinquefasciatus remains a substantial impediment to further progress in Culex biology and vector comparative genomics. Using PacBio sequencing, for which we have already assembled two Anopheles genomes de novo, we will reassemble Cx. quinquefasciatus and produce a significantly more contiguous assembly aided by both novel computational innovations and traditional physical mapping. The total number of scaffolds (pieces, also called supercontigs) will be reduced from 3171 to at most ~1750. In addition, this increase in assembly continuity will greatly augment the current cytogenetic map for Cx. quinquefasciatus and help anchor the majority of the genomic scaffolds (old, new or hybrid) to chromosomes. Although the primary goal of this R21 proposal is to significantly improve the genome assembly for Cx. quinquefasciatus, we undertake it with the long-term goal of piloting the sequencing and bioinformatics required to improve other important vectors (e.g., ongoing sandfly and black fly community efforts). The specific aims for this project are to: 1) improve the quality of the Cx. quinquefasciatus genome assembly through PacBio sequencing; 2) augment and improve this assembly using multicolor fluorescent in situ hybridization; and 3) innovate assembly improvement and comparison within and across mosquitoes. The availability of a high quality genome assembly for Cx. quinquefasciatus through VectorBase will greatly enhance research in vector biology.

 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，已对 30 多个物种进行了测序，并通过 NIAID 资助的生物信息学资源中心 (BRC) VectorBase 公开了它们的基因组。然而，致倦库蚊（淋巴丝虫病和脑炎病毒的主要载体）的基因组组装仍然是主要蚊子中碎片化程度最高的，其基因组中只有 13% 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载体比较基因组学进一步进展的重大障碍。使用 PacBio 测序（我们已经从头组装了两个按蚊基因组），我们将重新组装 Cx。 quinquefasciatus 并在新颖的计算创新和传统物理映射的帮助下产生明显更加连续的组装。支架总数（片段，也称为超级重叠群）将从 3171 个减少到最多约 1750 个。此外，装配连续性的增加将极大地增强 Cx 当前的细胞遗传学图谱。 quinquefasciatus 并帮助将大部分基因组支架（旧的、新的或混合的）锚定到染色体上。尽管这个 R21 提案的主要目标是显着改善 Cx 的基因组组装。 quinquefasciatus，我们开展这项工作的长期目标是试点改进其他重要载体所需的测序和生物信息学（例如，正在进行的白蛉和黑蝇社区努力）。该项目的具体目标是： 1) 提高 Cx 的质量。通过 PacBio 测序组装 quinquefasciatus 基因组； 2) 使用多色荧光原位杂交增强和改进该组装； 3）在蚊子内部和之间进行创新组装改进和比较。为 Cx 提供高质量的基因组组装。 quinquefasciatus 通过 VectorBase 将极大地加强媒介生物学的研究。