A linkage-based genome assembly for the mosquito Aedes albopictus and identification of chromosomal regions affecting diapause

The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (~1.19-1.28 Gb by cytofluorometric estimates), comprised of ~68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our re-assembled genome sequence, AalbF3, represents several improvements relative to AalbF2.  First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as reference for a bulk segregant-based comparative genomics analysis which identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of Ae. albopictus.

白纹伊蚊（Aedes albopictus，俗称亚洲虎蚊）是一类具有重大公共卫生隐患的入侵性媒介蚊类。该物种基因组规模庞大（经细胞荧光定量估算约为1.19~1.28 Gb），其中约68%为重复DNA序列，这使得构建该物种的高质量基因组组装面临极大挑战。本研究基于RNA测序（RNAseq）获得的111328个信息性单核苷酸多态性位点（SNPs），构建了白纹伊蚊的高密度连锁图谱。随后，我们对Palatini等人2020年发布的基因组组装版本AalbF2开展了基于连锁图谱锚定的重新组装工作。我们得到的重新组装基因组序列AalbF3相较于AalbF2存在多处优化：其一，AalbF3的组装规模为1.45 Gb，仅约为AalbF2的一半；其二，相较于AalbF2，AalbF3中完整且单拷贝的BUSCO基因占比更高（84.3%），且能以单一位点一致比对方式匹配的RNA测序读段比例也更高（46%）。我们通过将AalbF3作为参考基因组开展基于混合分群的比较基因组学分析，验证了该组装版本的实用性：该分析鉴定出了携带与光周期滞育相关的候选SNP簇的染色体区域，而光周期滞育是支撑白纹伊蚊快速范围扩张与气候适应性的关键生态适应性状。