Unified Culex assemblies for improved population-level analysis

 描述(申请人提供)：蚊子是多种传染病的传播者。为了促进先进的基于基因组的病媒控制策略的发展，已经对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公开提供了它们的基因组。然而，淋巴丝虫病蠕虫和脑炎病毒的主要媒介致倦库蚊的基因组组装仍然是主要蚊子中最高度碎片化的，只有13%的基因组被放置在染色体上。缺乏高质量的、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媒介比较基因组学进一步发展的重要障碍。使用PacBio测序，我们已经重新组装了两个按蚊基因组，我们将重新组装CX。在新的计算创新和传统的物理映射的帮助下，产生更连续的组件。支架(碎片，也称为超重叠群)的总数将从3171个减少到最多1750个。此外，这种组装连续性的增加将极大地增强目前CX的细胞遗传学图谱。并帮助将大多数基因组支架(旧的、新的或杂交的)固定在染色体上。尽管这项R21提案的主要目标是显着改善CX的基因组组装。作为Ququiefasciatus，我们进行这项工作的长期目标是试点改进其他重要媒介所需的测序和生物信息学(例如，正在进行的沙蝇和黑蝇群落努力)。该项目的具体目标是：1)提高CX的质量。Ququiefasciatus通过PacBio测序进行基因组组装；2)使用多色荧光原位杂交增强和改进这种组装；以及3)创新组装改进和蚊子内部和跨蚊子之间的比较。CX的高质量基因组组装的可用性。Ququiefasciatus通过VectorBase将极大地促进媒介生物学的研究。

 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.