Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti

Abstract

Background: 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. Results: 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.Conclusions: 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.

Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements

“…The repetitive nature of these sequences along with the lack of knowledge of the TE landscape in our samples prevented mapping of the CFAV‐EVE2 integration site. To overcome this issue, we mined data from linked‐read (10X Genomics) libraries (Redmond et al, 2020). This analysis identified a clean signal of a presumably single‐copy viral insertion around 461 MB on chromosome 2, at the far end of the q arm, in two mosquitoes from Africa (Figure ).…”

“…For those novel nrEVEs for which we could not identify the genome integration site by remapping the flanking regions to the A. aegypti genome, we investigated a set of 28 sequences, representing a broad geographical and genetic distribution of A. aegypti , that had been sequenced with linked‐read (10×) sequencing that generated libraries in which reads that derived from a single strand of DNA are tagged with a unique barcode to map the new nrEVE in the A. aegypti genome (Redmond et al, 2020). Comparison of common barcodes allows inference of proximity between reads up to 80 kb apart.…”

Genetic structure of the mosquito Aedes aegypti in local forest and domestic habitats in Gabon and Kenya

“…Further studies specifically focusing on this gene are needed to further confirm whether this gene was under diverging selection pressure related to habitats. Other possibilities that cause this peak of divergence include unaccounted external gene flow into the La Lopé populations, as well as possible chromosome inversions that accumulate genetic divergence [ 68 – 70 ]. This divergent genomic region was not found in the analysis of the Rabai populations (Fig.…”

Effect of Selection for Pyrethroid Resistance on Abiotic Stress Tolerance in Aedes aegypti from Merida, Yucatan, Mexico

“…Larval habitat salinity may also selectively influence the fitness of alternate populations by affecting factors such as body size, energy storage, or cuticular thickness in the adults. Associations between insecticide resistance and other fitness traits may result from genetic linkages, possibly within chromosomal inversions [ 72 ] or micro-inversions [ 73 ], such as have already been observed in Drosophila melanogaster [ 74 ] and Anopheles spp. [ 75 ].…”