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Improved mosquito reference genome assembly produced using long-read sequencing

PacBio technology enables new insights into biology of disease-carrying insect; could inform disease control strategies for major public health threat

Bioscribe

November 14, 2018 - A new comprehensive map of mosquito DNA has been assembled using long-read sequencing technology from California-based Pacific Biosciences. The improved reference genome assembly could help scientists combat the pest and infectious diseases it spreads, including Zika, dengue, chikungunya, and yellow fever.

In an unprecedented crowd-sourced effort stoked by social media, 72 scientists from around the world have collaborated to produce the new high-quality Aedes aegypti mosquito genome.

PacBio's Single Molecule, Real-Time (SMRT®) Sequencing enabled the team to read the DNA in long, uninterrupted segments, giving researchers a much more complete and accurate picture of gene elements and how they are positioned.

In a paper published today in Nature, lead author Leslie B. Vosshall, first author Benjamin Matthews, both of Rockefeller University, and colleagues at several other institutions, described how the new resource is a big improvement over the first Ae. aegypti genome created a decade ago.

Dr. Vosshall commented: "The field was being held back for lack of a high-quality genome. Partnering with PacBio made it possible for us to obtain high quality long-read sequences that enabled us to generate a platinum-quality genome assembly. The resulting annotated genome is really impressively complete and has already had a huge impact on the field, allowing scientists around to world to carry out a number of experiments that were previously impossible."

The Ae. aegypti genome is large (~1.3 Gb) and has many repetitive elements. Previous efforts suffered from shorter segment sequences that had to be pieced together, resulting in more than 30,000 gaps.

Using long-read SMRT Sequencing, Matthews et al. were able to dramatically reduce the number of segments needed to construct the genome, as well as the number of gaps. In fact, the new "AaegL5" reference genome, has a 93% decrease in the number of pieces, referred to as contigs (continuous lengths of genomic sequences). As a result, the scientists were able to validate local structure, predict structural variants between haplotypes (the strings of DNA inherited from each parent), and generate a much-improved gene set annotation.

"Female Ae. aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens," the authors write. "Progress in understanding mosquito biology and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly."

The new, more complete assembly has already revealed some of what biologists have been missing, and that information could be key to developing new strategies for pest control, the authors write.

One gene crucial for sex determination--the Nix gene--was entirely missing from previous Ae. aegypti assemblies, for example. Locating where this gene and the corresponding male-determining factor (M-factor) appear on the chromosome is important for scientists who wish to breed and release males into the wild as a way to bias the population towards males, rather than disease-transmitting females, over multiple generations.

The team identified 49 new genes involved in immune responses, blood protein digestion, and the maturation of oocyte reproduction cells, and they corrected gene models of 27 membrane receptors that respond to diverse external and internal sensory stimuli.

The new genome has also provided critical clues into how the insects sense a vast array of chemical cues, such as the carbon dioxide and human body odor that attracts female mosquitoes. Among them were 54 new ionotropic receptors (IRs), many linked to "taste" receptors in the legs that female mosquitoes use to find egg-laying sites.

"Characterization of the full chemosensory-receptor repertoire will enable the development of novel strategies to disrupt mosquito biting behaviour," the authors write.

Another important find was the location of markers that differentiated mosquitoes capable of transmitting certain viruses, like dengue. Other discoveries enabled by the new assembly could provide insight into insecticide resistance, as well as identify potential new candidates for insecticides. For example, by tracing ion channels, the team identified a type of insecticide widely used in agricultural and veterinary applications that could be repurposed to kill mosquito larvae.

Laura Harrington, a Cornell University entomology professor and director of the CDC Northeast Regional Center for Excellence in Vector-borne Diseases, who was not involved in the study, said: "Aedes aegypti is a tremendously important disease vector globally and we desperately need better strategies to minimize the public health impact of the infections it transmits. This new high-quality genome will dramatically accelerate our ability to develop new tools for prevention and control."

"The completion of this mosquito genome provides an enormous contribution to future global health efforts and may address the devastating diseases carried by this species, such as the Zika virus," said Jonas Korlach, Chief Scientific Officer of Pacific Biosciences. "SMRT Sequencing has been employed extensively in the study of infectious disease, particularly for the smaller genomes of viral and microbial pathogens. Recent performance improvements in the technology have also made it more cost effective to resolve the larger, more complex genomes of host species, providing a more complete picture of disease lifecycle. The methods used in this reference genome assembly create a path for producing high-quality reference assemblies for other challenging species."

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An infographic about how genome references like this mosquito accelerate science is available here: https://www.pacb.com/wp-content/uploads/Infographic-Gold-standard-reference-genomes-accelerate-science.pdf.

The study was funded in part by the National Institutes of Health, the National Science Foundation, Howard Hughes Medical Institute, the Jane Coffin Childs Memorial Fund, the Robertson Foundation, the McNair & Welch Foundations, the French government's Investissement d'Avenir program, and the European Union's Horizon 2020 research and innovation program.

About Pacific Biosciences

Pacific Biosciences of California, Inc. (NASDAQ:PACB) offers sequencing systems to help scientists resolve genetically complex problems. Based on its novel Single Molecule, Real-Time (SMRT®) technology, Pacific Biosciences' products enable: de novo genome assembly to finish genomes in order to more fully identify, annotate and decipher genomic structures; full-length transcript analysis to improve annotations in reference genomes, characterize alternatively spliced isoforms in important gene families, and find novel genes; targeted sequencing to more comprehensively characterize genetic variations; and real-time kinetic information for epigenome characterization. Pacific Biosciences' technology provides high accuracy, ultra-long reads, uniform coverage, and the ability to simultaneously detect epigenetic changes. PacBio® sequencing systems, including consumables and software, provide a simple, fast, end-to-end workflow for SMRT Sequencing. More information is available at http://www.pacb.com.

Media contact:

Media:

Nicole Litchfield
415.793.6468
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