Aedes aegypti is the principal mosquito vector of Zika, dengue, and yellow fever viruses. Two subspecies of Ae. aegypti exhibit phenotypic divergence with regard to habitat, host preference, and vectorial capacity. Chromosomal inversions have been shown to play a major role in adaptation and speciation in dipteran insects and would be of great utility for studies of Ae. aegypti. However, the large and highly repetitive genome of Ae. aegypti makes it difficult to detect inversions with paired-end short-read sequencing data, and polytene chromosome analysis does not provide sufficient resolution to detect chromosome banding patterns indicative of inversions. To characterize chromosomal diversity in this species, we have carried out deep Illumina sequencing of linked-read (10X Genomics) libraries in order to discover inversion loci as well as SNPs. We analyzed individuals from colonies representing the geographic limits of each subspecies, one contact zone between subspecies, and a closely related sister species. Despite genome-wide SNP divergence and abundant microinversions, we do not find any inversions occurring as fixed differences between subspecies. Many microinversions are found in regions that have introgressed and have captured genes that could impact behavior, such as a cluster of odorant-binding proteins that may play a role in host feeding preference. Our study shows that inversions are abundant and widely shared among subspecies of Aedes aegypti and that introgression has occurred in regions of secondary contact. This library of 32 novel chromosomal inversions demonstrates the capacity for linked-read sequencing to identify previously intractable genomic rearrangements and provides a foundation for future population genetics studies in this species.

中文翻译：

---

链接阅读测序可识别虫媒病毒载体埃及伊蚊中丰富的微倒位和基因渗入

埃及伊蚊是寨卡病毒、登革热病毒和黄热病病毒的主要蚊媒。Ae的两个亚种。埃及伊蚊在栖息地、寄主偏好和媒介能力方面表现出表型差异。染色体倒位已被证明在双翅目昆虫的适应和物种形成中起重要作用，并且对 Ae 的研究非常有用。埃及。然而，Ae 的大且高度重复的基因组。aegypti 使得使用双端短读长测序数据检测倒位变得困难，并且多线染色体分析无法提供足够的分辨率来检测指示倒位的染色体条带模式。为了表征该物种的染色体多样性，我们对linked-read（10X Genomics）文库进行了深度Illumina测序，以发现倒位基因座和SNP。我们分析了代表每个亚种的地理界限、亚种之间的一个接触区和一个密切相关的姐妹物种的群体中的个体。尽管全基因组 SNP 分歧和丰富的微倒位，我们没有发现任何倒位作为亚种之间的固定差异发生。在已经渗入并捕获可能影响行为的基因的区域中发现了许多微倒位，例如可能在宿主喂养偏好中起作用的一组气味结合蛋白。我们的研究表明，在埃及伊蚊的亚种中，倒位是丰富的和广泛共享的，并且基因渗入已经发生在二次接触的区域。