Comparative genomics of the 2La inversion breakpoints in Anopheles gambiae

描述（由申请人提供）：疟疾具有巨大的生物和社会复杂性，仍然是当今最重要的全球卫生问题之一。一种控制传染病的新方法是靶向负责媒介能力的基因。最有效的疟疾媒介冈比亚按蚊（Anopheles gambiae）的基因组具有许多与疟疾传播相关的特定适应性相关的染色体多态性。2La多态性反转是广泛存在的重要表型：恶性疟原虫感染率降低和对干旱气候的适应。我们提出了一个模型，其中2La反转的替代染色体排列通过捕获和稳定含有特定基因等位基因复合物的不同单倍型变体来影响载体的能力和对干旱的适应。我们控制这些“效应基因”的能力将导致对寄生虫发育的干扰，从而消除疟疾传播。本研究的长期目标是了解倒置多态性与流行病学上重要表型之间的关联机制，以便开发抑制寄生虫传播的新工具。最近对马里冈比亚疟蚊自然种群进行的遗传调查发现，在2La近端断点附近的一个小区域内，出现了最强的恶性疟耐药位点群。我们假设，i)抗性集群区域的2L臂排列之间存在异常高水平的结构差异，ii)抗性集群中的遗传变异，包括APL1和/或其他免疫相关基因的适应性变异，会影响疟疾易感性，从而影响自然中的生理媒介能力。同样，2L排列之间的等位基因分化可能是倒转多态性与适应干旱的关系的原因。本探索性R21项目的主要任务是对野生蚊子倒排和标准排列的疟原虫抗性岛进行详细的比较分析，以确定编码序列的差异。使用靶向重测序和新的超快速测序工具将为发现野生种群的基因组序列和结构提供新的方法。我们的研究获得的基因组片段的反向安排,第一次基因注释提供了一个广泛的临床流行病学和重要的染色体地区野生,non-colonized冈比亚按蚊自然种群。具体目的是：1)在采集的马里野生冈比亚伊蚊2La和2L+染色体的断点处获得约1.5-2 Mb的单倍体DNA序列，2)在2La和2L+染色体上标注预测编码序列，并对两种序列进行比较基因组分析，确定载体能力和生态适应的候选基因。公共卫生相关性：疟疾具有巨大的生物和社会复杂性，仍然是当今最重要的全球卫生问题之一。提出的研究将确定候选基因载体能力。我们控制干扰寄生虫发育的基因的能力将导致消除疟疾传播。

DESCRIPTION (provided by applicant): Malaria, with its great biological and social complexity, remains one of the most important global health problems today. One novel approach for controlling infectious diseases is targeting genes responsible for vector competence. The genome of the most efficient malaria vector, Anopheles gambiae, has a number of chromosomal polymorphisms linked to specific adaptations related to malaria transmission. The 2La polymorphic inversion is widespread important phenotypes: decreased Plasmodium falciparum infection rates and adaptation to arid climate. We propose a model where the alternative chromosomal arrangements of the 2La inversion affect vector competence and adaptation to aridity by capturing and stabilizing different haplotypic variants containing allelic complexes of specific genes. Our ability to control these "effector genes" would lead to interference with parasite development and, as a result, to elimination of malaria transmission. The long-term goal of this research is to understand the mechanism of association between inversion polymorphism and the epidemiologically important phenotypes in order to develop novel tools for inhibiting parasite transmission. A recent genetic survey of natural populations of A. gambiae in Mali has identified the strongest P. falciparum resistance loci cluster in a small region near the 2La proximal breakpoint. We hypothesize that i) there are unusually high levels of structural divergence between the 2L arm arrangements in the resistance cluster region, and ii) that genetic variation in the resistance cluster, including adaptive variation for APL1 and/or other immunity-related genes, influences malaria susceptibility and, therefore, physiological vector competence in nature. Similarly, allelic differentiation between the 2L arrangements could be responsible for association of the inversion polymorphism with adaptations to aridity. The major thrust of this exploratory R21 project is to perform detailed comparative analysis of the Plasmodium resistance island in inverted and standard arrangements from wild mosquitoes in order to identify differences in coding sequences. Using targeted resequencing with new, ultra-fast sequencing tools will provide novel methodology for the discovery of genome sequence and structure in wild populations. Our study of the genomic segments obtained from the inverted arrangements will, for the first time, provide for gene annotation over an extensive and epidemiologically significant chromosomal region in wild, non-colonized A. gambiae from a natural population. The specific aims are to: 1) Obtain ~1.5-2 Mb of haploid DNA sequences at both breakpoints of 2La and 2L+ arrangements from wild A. gambiae mosquitoes collected in Mali. 2) Annotate predicted coding sequences in 2La and 2L+ chromosomes, perform comparative genomic analysis of both sequence arrangements, and identify candidate genes for vector competence and ecological adaptation. PUBLIC HEALTH RELEVANCE: Malaria, with its great biological and social complexity, remains one of the most important global health problems today. The proposed research will identify candidate genes for vector competence. Our ability to control genes responsible for interference with parasite development will lead to the elimination of malaria transmission.