Every year, millions of people are bitten by the mosquito Aedes aegypti. Thousands die as a result of infection by the viruses the mosquito carries1, which can cause diseases such as yellow fever, dengue fever and Zika. Current mosquito-suppression methods typically involve pesticides. However, mosquitoes quickly develop resistance to these chemicals2, and pesticides can accumulate in the food chain, with adverse effects on beneficial insects, other wildlife and humans. New control methods are therefore needed. Writing in Nature, Matthews et al.3 describe a high-quality genome sequence for A. aegypti (Fig. 1). This exemplary work could be a major step towards addressing our current inability to manage expanding mosquito populations.
Arguably the most promising alternatives to pesticide-based mosquito control are targeted molecular strategies based on genetics. The first requirement for the success of such strategies is high-quality sequencing of the mosquito genome. This would enable researchers to identify gene targets that could be manipulated to achieve a range of effects: to disrupt the mosquito’s host-targeting systems; to make sterile males; to convert females into harmless males; or to render the insect incapable of harbouring viruses.
The repetitive nature of the 1.3-gigabase-long A. aegypti genome has severely hampered efforts to generate a high-quality sequence. Previous attempts4,5 resulted in patchy genomes that were assembled using short sequence reads. To overcome these challenges, Matthews et al. used next-generation sequencing to generate 166 Gb of long sequence reads with an average length of 17 kilobases. The authors used sophisticated mapping and gap-filling techniques to determine the positions of 94% of their sequence reads on the mosquito’s three chromosomes, successfully assembling 1.28 Gb of the genome. The assembly has many fewer gaps than previous assemblies, and is a 100-fold improvement in terms of its N50 — a statistical measure based on the median assembled DNA-sequence length.
With this assembly in hand, Matthews and colleagues were able to improve our knowledge of the sequences of thousands of genes, and to discover new members of existing gene families. For example, the researchers identified more than 300 genes that encode ligand-gated ion channels, which allow ions to pass through membranes. These genes fall into three classes of receptor: odorant, gustatory and ionotropic. Together, they sense a wide range of chemicals, including carbon dioxide and chemicals that emanate from humans. Matthews et al. identified 54 previously unknown genes encoding ionotropic receptors — almost doubling the number known before. These genes are ideal candidates to target for disruption, because they confer the mosquito’s ability to detect odours that indicate the presence of a host.
Of note, the authors identified 14 members of the best-studied subgroup of ionotropic receptors, nicotinic acetylcholine receptors, which act in the insect nervous system6. These receptors are the targets of insecticides called neonicotinoids, which have gained much attention owing to their adverse effects on beneficial insects such as bees. Knowing the sequences of the genes that encode these receptors should enable researchers to design insecticides that specifically target mosquitoes, sparing beneficial species.
Gene duplication is one mechanism by which insects can develop resistance to pesticides. Matthews et al. used their assembly to resolve a complicated gene-repeat region involved in one such resistance event. The region contains a cluster of three Glutathione S-transferase (GST) genes, which the authors found had been duplicated four times. These genes are important for metabolizing toxins, with one gene, GSTe2, capable of metabolizing the insecticide DDT. Increased expression of GSTe2 has been associated with DDT resistance in a laboratory-colonized A. aegypti strain7, supporting the idea that the gene duplication identified by the authors is involved in pesticide resistance. These data provide a proof of principle that the new genome will be an invaluable resource for researchers looking to analyse any gene family implicated in pesticide resistance.
Sex determination in A. aegypti is controlled by a sex-specific region called the M locus that is located on chromosome 1 in males only. It was known that the region contained the male-specific genes myo-sex and Nix, but they were absent from previous genome assemblies. This gap has been filled in the new genome. The authors estimate the M locus to be 1.5 megabases long (0.1% of chromosome 1), and show that it contains a much more repetitive sequence than does the rest of the genome — 73.7% compared with 11.7% genome-wide. The high repeat density is similar to that found in the Y chromosome of other animals8.
Apart from the M locus, the sequence of chromosome 1 is very similar in males and females. This type of chromosome structure is known as homomorphic. Matthews and colleagues’ genome will provide researchers with the opportunity to examine how the homomorphic sex chromosomes of A. aegypti are maintained, rather than evolving into heteromorphic chromosomes that are broadly different between the sexes — a better-understood phenomenon that is exemplified by the human X and Y chromosomes.
Finally, the authors used genetic-mapping techniques to identify regions of the genome that are associated both with the ability of mosquitoes to act as vectors for dengue virus and with resistance to the pesticide deltamethrin. The latter analysis highlighted candidate genes not previously known to be involved in pesticide resistance.
Even though Matthews and co-workers’ genome is a radical improvement on previous assemblies, important genes might still be missing, because there are a few thousand gaps in the main chromosomes, and large gaps spanning specialized structures called centromeres, to which proteins bind during cell division. Nonetheless, the authors’ sophisticated genome-sequencing strategy should act as a template for future efforts to assemble complex genomes. The genome and the gene sets themselves are publicly available for others to use (see go.nature.com/2dc6kxp), and, thanks to genome-editing technologies such as CRISPR–Cas9, researchers will easily be able to explore the effects of disrupting each gene identified as a candidate for targeting.
The use of tools rooted in genomic analysis and manipulation is a key step towards a pesticide-free world. Matthews and colleagues’ work makes a major contribution to this goal.
Nature 563, 482-483 (2018)