Anchoring and uniting the An. funestus assembly for improved vector analysis

描述（由申请人提供）：团结和统一安。用于改进的矢量分析的funestus组件。不死按蚊是热带非洲三种最重要和最广泛的人类疟疾媒介之一，但与按蚊不同。虽然它与冈比亚广泛共存，但它是一个相对被忽视的物种。它与安共享。冈比亚按蚊不仅广泛分布于撒哈拉以南地区和主要病媒地位，而且在非洲大部分地区还具有丰富的染色体倒位多态性和明显的浅种群结构。然而，对疟疾传播相关的行为和遗传异质性仍然知之甚少。在西非的热带稀树草原上，20世纪60年代残留杀虫剂的应用并不成功。与非洲其他地方一样，有强有力的细胞遗传学证据表明，在同一个村庄里共同发生了神秘的、暂时稳定的交配种群。与An的染色体形式明显相似。gambiae，染色体识别的An.被命名为Kiribina和Folonzo细胞型的funestus似乎在幼虫生态学上有所不同。重要的是，它们在影响矢量能力的成年行为上也有差异，最明显的是室内/室外休息行为。目前，存在 没有快速的分子鉴定分析，以促进更深入的实地研究，他们的行为和遗传学;细胞型只能区分费力的染色体核型分析。我们的长期目标是了解在流行病学上重要的表型和行为特征在An的潜在基因组决定因素。funestus及其细胞类型。最新发布的An。funestus基因组开始使这一目标成为可能，但其不固定在染色体上的碎片状态构成了一个障碍，阻碍了影响感兴趣性状的因果基因座的鉴定。这个R21的中心目标是升级An草案。funestus参考了基于染色体的组装，其中未锚定的支架在染色体臂上联合、有序和定向，使得能够初步评估细胞型之间的基因组差异。为此，我们提出三个具体目标：1。通过物理作图将组装体与细胞遗传学图谱整合。2.使用单分子测序对未锚定的支架进行连接、排序和定向。3.评估一个人之间的分歧。funestus cytotypes通过基因组扫描。将强大的新测序技术与传统的染色体物理映射相结合的创新策略将把参考草案转化为基于染色体的组装，并提供在An中发现的手段。funestus和它的细胞类型的遗传基础的性状，影响疾病的传播。

DESCRIPTION (provided by applicant): Anchoring and uniting the An. funestus assembly for improved vector analysis. Anopheles funestus is one of the three most important and widespread vectors of human malaria in tropical Africa, but unlike An. gambiae with which it broadly co-occurs, it is a relatively neglected species. It shares with An. gambiae not only a broad sub-Saharan distribution and major vector status, but also abundant chromosomal inversion polymorphism and apparently shallow population structure across much of Africa. However, there are behavioral and genetic heterogeneities relevant to malaria transmission that remain poorly understood. In the savannas of West Africa, where application of residual insecticides in the 1960's was not as successful against An. funestus as elsewhere in Africa, there is strong cytogenetic evidence for cryptic, temporally stable assortatively mating populations co-occurring in the same villages. In apparent analogy to the chromosomal forms of An. gambiae, the chromosomally recognized forms of An. funestus, named Kiribina and Folonzo cytotypes, seem to differ in larval ecology. Importantly, they also differ in adult behaviors affecting vectorial capacity, most notably indoor/outdoor resting behavior. At present, there exist no rapid molecular identification assays to facilitate more in-depth field studies of their behavio and genetics; the cytotypes can only be distinguished by laborious chromosomal karyotyping. Our long-term goal is to understand the underlying genomic determinants of epidemiologically important phenotypic and behavioral traits in An. funestus and its cytotypes. The newly sequenced An. funestus genome begins to make possible this goal, but its fragmented state, unanchored to chromosomes, poses a barrier that hinders the identification of causal loci affecting traits of interest. The central goal of this R21 is to upgrade the draft An. funestus reference to a chromosome-based assembly in which the unanchored scaffolds are united, ordered and oriented on chromosome arms, enabling a preliminary assessment of genomic divergence between the cytotypes. Toward this end, we propose three specific Aims: 1. Integrate the assembly with the cytogenetic map by physical mapping. 2. Unite, order and orient unanchored scaffolds using single molecule sequencing. 3. Assess divergence between An. funestus cytotypes by genome scans. The innovative strategy of integrating a powerful new sequencing technology with traditional physical mapping to chromosomes will transform the draft reference into a chromosome-based assembly, and provide the means to uncover in An. funestus and its cytotypes the genetic basis of traits that affect disease transmission.