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

描述（由申请人提供）：锚定和联合An。用于改进矢量分析的Funestus组件。funestus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。它与冈比亚虫广泛共存，是一个相对被忽视的物种。它与An共享。冈比亚虫不仅在撒哈拉以南地区分布广泛，是主要的病媒，而且在非洲大部分地区具有丰富的染色体倒位多态性和明显的浅种群结构。然而，与疟疾传播有关的行为和遗传异质性仍然知之甚少。在西非的稀树大草原上，20世纪60年代使用残留杀虫剂对付安虫并不成功。与非洲其他地方一样，有强有力的细胞遗传学证据表明，在同一村庄中，同时出现了隐型的、暂时稳定的、选择性交配的种群。在明显的类似于染色体形式的An。冈比亚，染色体识别形式的安。被命名为基里比纳和福隆佐细胞型的funestus似乎在幼虫生态学上有所不同。重要的是，它们在影响媒介容量的成人行为方面也存在差异，最明显的是室内/室外休息行为。目前是存在的

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.