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

Authors :
Seth N. Redmond
Atashi Sharma
Igor Sharakhov
Zhijian Tu
Maria Sharakhova
Daniel E. Neafsey
Source :
BMC Biology, Vol 18, Iss 1, Pp 1-14 (2020)
Publication Year :
2020
Publisher :
BMC, 2020.

Abstract

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.

Details

Language :
English
ISSN :
17417007
Volume :
18
Issue :
1
Database :
Directory of Open Access Journals
Journal :
BMC Biology
Publication Type :
Academic Journal
Accession number :
edsdoj.9d6e66fc965a4c10a3c26a3de0503716
Document Type :
article
Full Text :
https://doi.org/10.1186/s12915-020-0757-y