Inside the Sprint to Map the Asian Giant Hornet Genome

“Sequencing the Asian giant hornet genome has been a real pushing-the-envelope sort of project for us,” says Anna Childers, a computational biologist with the USDA’s Agricultural Research Service, or ARS. Childers works in the agency’s Bee Research Lab in Beltsville, Maryland, and leads its genome assembly group. Since 2011, scientists at the agency have been sequencing agriculturally important arthropods—not just bees, but flies, ticks, beetles, and lots of other bugs, too—as part of the agency’s contribution to the “i5k” initiative, itself one arm within a planet-scale sequencing moon shot known as the Earth BioGenome Project.

I5k’s goal was to catalog the genomes of 5,000 species within five years. But as of yet, the sequences of only 78 organisms have been completed, according to the initiative’s database. Insect genomes, it turned out, proved particularly challenging to map. For one thing, their chitin-covered bodies are small, so there’s often not much genetic material to work with. That leads to more errors and patchier sequences. Complicating matters further, some bugs actually have molecules in their eyes that block the action of the enzymes that sequencing machines employ to build and read genes.

More recently, sequencing companies like Pacific Biosciences and Oxford Nanopore have developed newer technologies to surmount some of these challenges. In 2018, ARS decided to combine some of these new methods with the hard-earned insect sequencing expertise the agency had gained over the past few frustrating years into a new effort targeted at the bugs that pose the biggest threat to the nation’s crops, livestock, bees, and trees. The Ag100Pest Initiative, as it is known, originally aimed to provide reference-quality genome sequences for the worst 100 of these nuisance insects, though the tally has since grown to 134. ARS scientists published their first genome off the list last year—that of the spotted lanternfly, another invasive that has decimated vineyards and orchards in the Northeast US. Their next project is the desert locust, city-size swarms of which are right now causing a dual disaster of plagues in Africa.

Initially, the Asian giant hornet didn’t make the USDA’s list, because in 2018 no one had ever seen one in North America. Its native range extends west from northern India to Japan, and from Russia’s Far East heading south to Thailand and Vietnam. Even when the first North American specimen was discovered last summer in British Columbia, Childers says there wasn’t much appetite at the agency for trying to get a sample to sequence. “People thought it was probably just a stray,” she says. But then, in August, beekeepers in the town of Nanaimo, on Vancouver Island, came across three more, which led them to a nest. And before they destroyed it, they managed to collect samples—four dinner plate-sized combs containing developing hornets, 200 workers, and the queen.

By early September, five of those hornets, all workers, had made their way into the freezer at Leonard Foster’s lab at the University of British Columbia. Foster runs the university’s proteomics core, and he’s also, as he puts it, “nearly the only bee researcher in British Columbia.” He was holding onto the insects for safekeeping, in the unfortunate event that more nests were found. Then the DNA inside their frozen cells would become important for comparing the original Nanaimo discoveries against other sites of invasion—to track their spread across the continent through subtle differences in their genetics.

Over the winter, another hornet was photographed in White Rock, on mainland British Columbia. Two more were found near Blaine, Washington, about 10 miles away, across the Canada–US border. Reports of suspicious beehive massacres in the area also began to appear. The threat of a hornet invasion was looking more and more real. Childers’ team kicked into high gear to figure out what they could do to help. In April, they got lucky. Someone at the USDA put her in touch with Foster, a long-time agency collaborator. He agreed to send her one of his specimens.