Improved Mosquito Reference Genome Supports Research into Deadly Diseases

Caption: Ben Matthews contemplates an Aedes aegypti mosquito.

More than 400 million people worldwide are infected each year by viruses carried by female Aedes aegypti mosquitoes. Until recently, research into disease transmission and mosquito biology was stymied by the lack of a reliable genome. The known fragments were not enough to untangle the complicated biological mechanisms behind the public health crises caused by dengue fever, yellow fever, and Zika. In 2018, former JCC Fellow Ben Matthews and his advisor Leslie B. Vosshall at The Rockefeller University, and more than 70 collaborators around the world published a much-improved mosquito reference genome.

Ben earned a BS in biology from the California Institute of Technology in 2004 and a PhD in Neurobiology and Behavior from Columbia University in 2010, where he worked in the laboratory of Wes Grueber on the mechanisms of dendrite self-avoidance mediated by the Dscam gene. He joined the Vosshall Lab in September 2010 and received a 2010 Henry and Marie Josee Kravis Postdoctoral fellowship and a 2011 Jane Coffin Childs Postdoctoral fellowship. Ben developed CRISPR-Cas9 gene-editing in the mosquito and has produced comprehensive genomic and transcriptomic resources to better understand mosquito biology.

Here, Matthews shares the impact of this research, as well as his experiences working on such an ambitious project.

What’s the significance of having this genome available for future research?

Matthews: Mosquitoes are vectors of deadly diseases, and Aedes aegypti in particular is responsible for hundreds of thousands of cases of arboviral disease (Dengue, yellow fever, and Zika) per year. Mosquito control increasingly relies on understanding the genetics and genomics of the mosquito, both to understand myriad aspects of basic mosquito biology and to develop potential interventions. The roadmap of an assembled and annotated genome is essential to these goals, and the old genome assembly was holding us back because we were not confident that it was complete and accurate. When we first put out feelers to the community about potential interest in a new genome assembly, we received a lot of responses from people interested in a wide range of aspects of mosquito biology indicating that the previous genome assembly (first published in 2007) was holding them back as well. The 2007 assembly was incredibly useful but was hampered by the state of sequencing technology and genome assembly tools of the time, and as a result was highly fragmented and incomplete. This was exacerbated by the fact that it is a very tricky genome to work with! It’s very large and repetitive as compared to some other insects (like the fruit fly, for example), and so required a lot of optimization to get our assembly as complete and accurate as possible.

What are some of the mosquito biology research questions that the new genome is helping to address?

Matthews: The genome can help improve our understanding of the chemosensory systems that mosquitoes use to find and bite human beings, identify suitable egg-laying sites, and more. We focused quite a bit on annotating the receptor gene families that encode taste and smell receptors in the mosquito, which will be useful for understanding which genes are important for specific behaviors. These genes are also potential targets for developing novel repellents and traps to control mosquito biting and population levels.

It can also aid in the development of insecticide resistance. As we deploy pyrethroids and other insecticides, mosquitoes and other insects develop resistance. Understanding what specific mutations are correlated with this resistance is critical to deploying the appropriate treatments in a specific area as well as designing novel insecticides that can get around these resistances

It’s also helping us understand mosquitoes’ competence to spread specific viruses. Some mosquito populations are better than others at spreading certain strains or serotypes of virus, and understanding why this is can potentially help to design drugs or other interventions that would help limit the spread of virus, or at least understanding the local spread of disease.

And you’re also using the genome to develop tools to further mosquito biology research?

Matthews: Having a well assembled and annotated genome is also critical for developing genetic tools to study mosquito biology and also potentially for release as a control mechanism (for example, modifying mosquitoes to make them less efficient at disease transmission, known as gene drive). A large part of my postdoctoral work in the Vosshall lab was focused on developing tools to manipulate the mosquito genome (CRISPR/Cas9) and study neural circuits in mosquitoes. This allows us to knockout specific genes to ascertain their role in particular behaviors, and design reagents for labeling and imaging neural activity in specific populations of neurons. This helps us understand how the mosquito nervous system translates sensory cues (for example, the smell of a human or the taste of an egg-laying site) into specific behaviors. To design these tools and reagents, you need to have a complete and accurate representation of the genome and the genes for a given species!

Is your study relevant to research beyond the field of mosquito biology?

Matthews: Beyond the mosquito field, our hope was that our paper provides an to-do list for how to assemble difficult and complex genomes using the variety of new sequencing technologies and tools. We generated a lot of data and did a lot of work to identify the best ways to integrate that data to produce the most complete and accurate final product, and the hope is that we can save others that time and cost by providing some simple rules-of-thumb. Many fields of biology are moving beyond traditional ‘model organisms’ (zebrafish, fruit fly, mouse) and asking questions that can only be addressed in a particular species, and having a genome assembly is an important step for many of these research programs. Thus, if we can help others by providing some guidance on how best to assemble complicated and repetitive genomes, that would be great! This field is moving so quickly, and I’m really gratified to already see advances beyond the methodology that we used – for example, while we had to use 80 siblings to get enough DNA to create our assembly, one of our colleagues, Sarah Kingan, and colleagues just showed that you can now approach those types of results from a single animal. This has huge implications for working with species where it’s hard to breed in the lab or other situations where you need to get the genome of individual animals.

Dr. Vosshall gauged interest among the research community on Twitter, and then assembled a team of co-authors. How did you manage a project with 72 collaborators?

Matthews: Leslie and I did a lot of project management, and I would say that the best way we found to deal with that many collaborators was to compartmentalize aspects of the paper. Each of the biological ‘vignettes’ that are presented in the latter half of the paper were spearheaded by a small subset of our authors, in coordination with Leslie and myself. We then had the task of combining everything into a single set of figures and text, which we would distribute to everyone for comments. This continued for a few rounds before peer review until we had a product that we were happy with. At that stage, we posted it on bioRxiv as a pre-print and submitted it to the journal. Once we had peer reviews, we would take specific comments and work with small groups of authors to address each one before again compiling the entire manuscript and sending around for comment.

What was the most exciting aspect of this project?

Matthews: To me, the most exciting part was to bring together people from a wide variety of fields in the service of a common goal: mosquito neurobiologists, experts on genomics, vector biologists, genome assembly experts, companies interested in developing new sequencing technologies, etc.

Looking forward, I’m excited by the idea that science is not limited to the classical suite of model organisms anymore. With the advent of cheaper and more complete genome assemblies in combination with tools like CRISPR/Cas9 that let you manipulate the genome of many different species, we can study unique aspects of biological life that cannot be modeled in, for example, a mouse or a fruitfly. As one concrete example: mosquitoes find and bite human beings, and turn their eggs into blood which they then lay near water. Fruit flies do none of those things, so we can’t really even scratch the surface of these behaviors work, mechanistically speaking, if we limit ourselves to ‘modeling’ them in Drosophila. This extends to other organisms with unique biology as well, and it’s a really exciting time for biologists who are interested in expanding the horizons in terms of study systems.

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