Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with a high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the second phase of a project to build an open resource of high-quality data on genome variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii. We analyzed whole genomes of 1142 individual mosquitoes sampled from the wild in 13 African countries, as well as a further 234 individuals comprising parents and progeny of 11 laboratory crosses. The data resource includes high-confidence single-nucleotide polymorphism (SNP) calls at 57 million variable sites, genome-wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We use these data to analyze genetic population structure and characterize genetic diversity within and between populations. We illustrate the utility of these data by investigating species differences in isolation by distance, genetic variation within proposed gene drive target sequences, and patterns of resistance to pyrethroid insecticides. This data resource provides a foundation for developing new operational systems for molecular surveillance and for accelerating research and development of new vector control tools. It also provides a unique resource for the study of population genomics and evolutionary biology in eukaryotic species with high levels of genetic diversity under strong anthropogenic evolutionary pressures.

中文翻译：

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非洲疟疾媒介物种冈比亚按蚊和科鲁兹按蚊的 1142 只蚊子的基因组变异和种群结构

蚊子控制仍然是减少撒哈拉以南非洲疟疾负担的核心支柱。然而，杀虫剂耐药性在疟疾媒介人群中根深蒂固，疟疾负担高的国家面临着通过有限的监测和干预工具维持疟疾控制的艰巨挑战。在这里，我们报告了一个项目的第二阶段，该项目旨在建立一个关于非洲主要疟疾媒介物种冈比亚按蚊和科鲁齐按蚊自然种群之间基因组变异的高质量数据的开放资源。. 我们分析了从 13 个非洲国家的野外采集的 1142 只蚊子的全基因组，以及另外 234 只蚊子的全基因组，其中包括 11 个实验室杂交的父母和后代。数据资源包括 5700 万个可变位点的高置信度单核苷酸多态性 (SNP) 调用、全基因组拷贝数变异 (CNV) 调用和双等位基因 SNP 分阶段的单倍型。我们使用这些数据来分析遗传种群结构并描述种群内部和种群之间的遗传多样性。我们通过调查距离隔离的物种差异、提议的基因驱动目标序列内的遗传变异以及对拟除虫菊酯杀虫剂的抗性模式来说明这些数据的效用。该数据资源为开发新的分子监测操作系统和加速新病媒控制工具的研究和开发奠定了基础。它还为在强大的人为进化压力下研究具有高水平遗传多样性的真核物种的种群基因组学和进化生物学提供了独特的资源。