Linkage map anchored genome reassembly and diapause associated SNPs in Aedes albopictus

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 reassembled 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 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 associ-ated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of Ae. albopictus.