Comparative genome mapping of the Anopheles species cluster

描述（由申请人提供）：靶向负责媒介能力的基因是控制传染病的新方法。为了更好地了解媒介能力的遗传决定因素，并在媒介生物学家和疟疾界成员的支持下，NHGRI和NIAID资助了16种按蚊的基因组和转录组测序（http://www.broadinstitute.org/annotation/genome/anopheles）。随着基因组序列的出现，研究人员现在有了独特的机会来进行比较分析，以推断与载体能力相关的进化变化。然而，这些比较基因组分析的成功将是有限的，如果研究人员处理大量的测序支架而不是基于染色体的基因组组装，那么关于载体能力性状进化的推断将会信息量更少。这个R21项目的主要目标是为三种主要的疟疾病媒开发基于染色体的参考基因组组合：arabiensis,。stephensi和An。albimanus。这些物种可获得基因组组装草图（https://olive.broadinstitute.org/comparisons/anopheles.1）。我们的项目很及时，因为它将为新测序的按蚊物种创造关键的基因组工具。该项目具有创新性，因为它将使用自动多色荧光原位杂交（AM-FISH）和自动显微分析。我们将首次通过全基因组基因顺序分析对按蚊进行系统发育分析，并对染色体重排的模式和机制获得重要的见解。最先进的设备和PI在细胞遗传学和比较基因组分析方面的专业知识的可用性将确保项目目标的成功实现。该提案有三个具体目标。具体目标将测序支架物理映射到An的染色体上。arabiensis,。stephensi和An。albimanus。我们将通过AM-FISH将支架放置和定向到多染色体染色体上，从而分别为属于Pyretophorus系列（celllia亚属），Neocellia系列（celllia亚属）和Albimanus系列（Nyssorhynchus亚属）的物种创建基于染色体的参考基因组组装。具体目标2。重建按蚊属的基因组尺度重排系统发育。我们将确定An中所有固定反转的断点。阿拉比亚种的染色体系统发育将进一步完善。冈比亚复合体使用An。斯蒂芬尼和安。作为外群种的白蛉。具体目标3。确定按蚊属染色体进化的模式和机制。我们将检验以下假设：(i)尽管缺乏反转多态性，但X染色体具有最高的反转固定率，以及（ii）反转具有染色体特异性和物种特异性的起源机制和固定率。！

DESCRIPTION (provided by applicant): Targeting genes responsible for vectorial capacity is a novel approach to controlling infectious diseases. To develop a better understanding of genetic determinants of vectorial capacity and with support from vector biologists and members of the malaria community, NHGRI and NIAID have funded the sequencing of the genomes and transcriptomes of 16 Anopheles species (http://www.broadinstitute.org/annotation/genome/anopheles). With genome sequences becoming available, researchers now have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, success of these comparative genomic analyses will be limited, and inferences about evolution of the vectorial capacity traits will be less informative if researchers deal with numerous sequencing scaffolds rather than with chromosome-based genome assemblies. The major goal of this R21 project is to develop chromosome-based reference genome assemblies for three major malaria vectors: An. arabiensis, An. stephensi, and An. albimanus. Draft genome assemblies are available for these species (https://olive.broadinstitute.org/comparisons/anopheles.1). Our project is timely because it will create crucial genomic tools for the newly sequenced Anopheles species. The project is innovative because it will use the automated multicolor fluorescent in situ hybridizatio (AM-FISH) and automated microscopic analysis. We will, for the first time, perform phylogenetic analysis of anopheline mosquitoes by genome-wide gene order analysis and gain important insights into patterns and mechanisms of chromosomal rearrangements. The availability of state-of-the-art equipment and the expertise of the PI in cytogenetics and comparative genomic analysis will ensure successful achievement of the project's goal. The proposal has three specific aims. Specific Aim 1. Physically map sequencing scaffolds to chromosomes of An. arabiensis, An. stephensi, and An. albimanus. We will place and orient scaffolds to polytene chromosomes by AM-FISH, thus, creating chromosome-based reference genome assemblies for the species belonging to the series Pyretophorus (subgenus Cellia), series Neocellia (subgenus Cellia), and series Albimanus (subgenus Nyssorhynchus), respectively. Specific Aim 2. Reconstruct genome-scale rearrangement phylogeny of genus Anopheles. We will identify breakpoints of all fixed inversions in An. arabiensis and will refine the chromosomal phylogeny in the An. gambiae complex using An. stephensi and An. albimanus as outgroup species. Specific Aim 3. Determine the pattern and mechanisms of chromosome evolution in genus Anopheles. We will test the hypotheses that (i) the X chromosome has the highest rate of inversion fixation despite the paucity of inversion polymorphisms, and (ii) inversions have chromosome-specific and species-specific mechanisms of origin and rates of fixation. !