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.