Rusty-patched bumble bees (Bombus affinis), are crucial pollinators of wildflowers and crops, like apples and cranberries. Named after the reddish patch on its back, the insect was listed as federally endangered in 2017.

Experts estimated that numbers have declined by 87 percent in the last two decades. Before its population declined, rusty-patched bees were found in prairies, woodlands, farms, gardens and parks across the eastern U.S., the upper Midwest and parts of Canada.

In a recent study published in G3 Genes|Genomes|Genetics, researchers sequenced the bee’s entire genome to understand its decline and how it affects the bee’s biology. The genetic map of the rusty-patched bee’s genome may be the key to saving the species.

“We have an opportunity to find a whole different approach to strengthening rusty patched bumble bee populations,” says Jonathan B. Uhaud Koch, study author and entomologist with the ARS Pollinating Insect-Biology, Management, Systematics Research Unit in a statement.

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A Vulnerable Species 

The exact cause for the species’ decline is unknown, but entomologists suspect some contributing factors are introduced pathogens and pesticides like insecticides and fungicides. Other factors like habitat loss and climate change may have contributed, too.

The few remaining pockets of the population face these stressors that hit synergistically or one at a time. For example, when bees can’t find enough resources for nectar, they are less likely to resist other stressors like pathogens or pesticides. A rusty-patched bee colony needs a constant supply and diversity of flowers blooming from April through September.

Finding the Parasitic Fungi

In the study, scientists sequenced the genome from abdominal tissue taken from one male rusty-patched bee caught from Minnesota’s wild outdoors. The team created high-quality genome maps from the single tissue sample detailing its 15,252 genes and 18 chromosomes. Because only a small sample of the bee was needed, researchers could keep most of the bee intact so that it could be later used for additional research or species confirmation, if required.

Aside from sequencing the genetic data, Koch found a surprising amount of genetic material from the fungal pathogen, Vairimorpha bombi. The pathogen is known to affect various species of bees and is a leading factor of the bee’s decline. Of the total DNA Koch and his colleagues sequenced, 4.5 percent was from Microsporidia, the same group of parasitic fungi that includes V. bombi.

“That’s a massive amount of genetic information from the bee tissue sample to be associated with Varimorpha bombi. It demonstrates how pervasive the pathogen is,” Koch says.

A Bee’s Genome

The achievement was part of the Beenome 100, a project set to create high-quality maps of the genomes of at least 100 bee species in the U.S. that represent the major taxonomic groups of insects found nationwide. In total, there are about 4,000 native bee species. The maps will help scientists understand genetic differences that make some bee species more vulnerable to climate change than others or which ones are more likely to be affected by a pesticide.

Since the USDA Agricultural Research Service leads the project, it allows the public to have access to the mapped genomes, and researchers then can get to work decoding each gene’s specific function.

“Having this high-quality genome will support the identification of genetic differences between rusty-patched bumble bee populations that appear to be doing well versus where they are in decline,” Koch says. “This may give us a handle on identifying the genes that give the more capable population its flexibility to deal with its environment.”

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