Unified Culex assemblies for improved population-level analysis

 描述（由申请人提供）：蚊子是许多传染病的媒介。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，并且通过NIAID资助的生物信息学资源中心（BRC）VectorBase提供了它们的基因组。然而，致倦库蚊（Culex quinquefasciatus）的基因组组装（其是淋巴丝虫病蠕虫和脑炎病毒的主要载体）仍然是主要蚊子中最高度片段化的，其基因组仅13%被置于染色体上。缺乏一个高质量的，基于染色体的基因组组装的Cx。致倦库蚊是库蚊生物学和媒介比较基因组学研究的重要障碍。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。quinquefasciatus，并产生一个显着更连续的组装，由新的计算创新和传统的物理映射的帮助。支架（片段，也称为超重叠群）的总数将从3171减少到最多约1750。此外，这种装配连续性的增加将极大地增强当前Cx的细胞遗传学图谱。并帮助锚大多数的基因组支架（旧的，新的或杂交）染色体。虽然R21提案的主要目标是显着改善Cx的基因组组装。quinquefasciatus，我们承担它的长期目标是试点测序和生物信息学需要改善其他重要的载体（例如，正在进行的白蛉和黑蝇社区工作）。该项目的具体目标是：1）提高Cx的质量。通过PacBio测序进行致倦犬基因组组装; 2）使用荧光原位杂交扩增和改进这种组装;和3）创新组装改进和蚊子内部和之间的比较。Cx高质量基因组组装的可用性。通过VectorBase将大大加强媒介生物学的研究。

 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.