Saving the Honey Bee: Can New Genomic Clues Help Solve the Colony Collapse Mystery?

Image credits:
Daniel Olaleye.

Colony collapse disorder has been the scourge of U.S. beekeepers for more than a decade, contributing to a 30-40 percent plunge in commercial honey bee colonies since 2006. A threat to bees is a threat to people: bees help pollinate more than one-third of our crops, including almonds, apples, cucumbers, melons and squash. Their labors as pollinators produced $15 billion worth of crops in the United States in 2016 alone, according to the U.S. Department of Agriculture.

Scientists initially struggled to explain colony collapse disorder. But through careful detective work, they have identified a parade of horribles that may trigger the fatal syndrome, including climate change, pesticides and bee parasites – yet in order to save the bees, scientists need more than just identify the culprits. They need detailed genomic, cellular and physiological data on how these factors imperil bee health, and how the damage can be stopped.

One parasite to rule them all

For the western honey bee, no parasite is more destructive than the Varroa mites — Varroa destructor and Varroa jacobsoni. These tiny ectoparasites bite both free-flying worker bees and larvae in the hive. Scientists originally believed that Varroa mites feed on hemolymph, the bee equivalent of blood. However, newer research indicates that they may instead prefer a liver-like organ in bees known as the fat body. But their appetite explains only part of the havoc that these mites wreak: Varroa bites also deliver a horde of debilitating and fatal viral pathogens that can ultimately doom a bee colony to extinction.


Proximo Hi-C on the case

An international team of scientists led by Dr. Maéva Techer and Dr. Alexander Mikheyev at the Okinawa Institute of Science and Technology employed Proximo Hi-C to obtain complete genomes for V. destructor and V. jacobsoni — picking up genomic regions missed in previous versions of the V. destructor genome and assembling the first-ever complete genome for V. jacobsoni.

“Understanding the mechanisms of parasitism requires detailed information about the organization of the genome,” said Dr. Mikheyev.

Already, they have identified regions of both genomes that proved essential for Varroa mites to parasitize honey bees. The team hopes that these new and improved genomic tools will ultimately reveal cellular or physiological traits in Varroa that scientists could exploit at the molecular level to save honey bee colonies from infection and destruction.

“Our company’s mission is to empower genomic researchers to make breakthrough discoveries,” said Dr. Ivan Liachko, founder and CEO of Phase Genomics, which performed the analysis. “Our technology brings unique benefits to the field of genome assembly and we are very proud to be a part of a project of such global importance as this endeavor to help honey bees.”

The case of the blighted western honey bee

Fighting Varroa is a particularly crucial issue for the western honey bee, Apis mellifera, a relatively new host for Varroa mites. Varroa mites and their original hosts — the eastern honey bee, Apis cerana — are native to Asia, while the western honey bee hails from Varroa-free Europe. But when beekeeping practices brought eastern and western honey bees together in the 19th and 20th centuries, V. destructor jumped from eastern honey bees to their western counterparts and eventually spread globally. Over the past 20 years, V. jacobsoni has also started to infest western honey bee hives in Asia.

Western honey bees are particularly vulnerable to Varroa mites because they lack the behavioral, chemical and immune-based strategies of their eastern cousins to resist or tolerate infestation. The Varroa genomes harbor just the type of detailed information scientists need to help western honey bees.

Varroa mites take the lonely road to parasitism

In their first look at the new V. jacobsoni and improved V. destructor genomes, the team found something unexpected.

“The evolutionary trajectories of both mites, despite their similarities and close relatedness, were completely dissimilar,” said Dr. Mikheyev.

Both genomes had more than 200 genes under positive selection, sure signs of recent adaptation to their bee hosts. But less than 10 percent of the genes under positive selection in V. destructor were also under positive selection in V. jacobsoni. The researchers also discovered tandem duplications in dozens of genes, something they could only see using Hi-C. But again, there was high divergence between the Varroa species. About 63 percent of duplications were found only in the V. destructor genome, and just under half were unique to V. jacobsoni.

Some of the genes under selection or duplication in V. destructor were involved in cellular processes such as RNA splicing, alcohol response, membrane depolarization, and development of myofibroblasts and retinal cells. High-selection or duplicated genes in V. jacobsoni were involved in mitochondrial protein processing, vitamin K metabolism, pH response, and gonad development. The two Varroa species, it seems, took different cellular routes to bring bees to heel.

Despite these differences, many genes under positive selection in one or both Varroa species are involved in the same general physiological properties, such as metabolizing toxins, which could play a role in developing resistance to miticides. Genes undergoing duplication or positive selection in both Varroa mites are also involved in stress tolerance, molting, nutrition and reproduction.

From past to future

Image credits: Eric Ward.

This initial study is a work of history — revealing the genes under positive selection or duplication due to past and present selective forces on Varroa mites. Scientists need this detailed bounty of level of genomic data to help develop effective anti-Varroa measures.

“Curiously, in both species, genes involved in stress tolerance and detoxification were already under selection,” said Dr. Mikheyev. “This most likely happened before they ever faced miticides and suggests that they may have pre-adapted strategies for dealing with our chemical warfare strategies against them.”

The researchers have made both Varroa genomes publicly available, so other teams can mine the sequences for additional data about the evolution, adaptation and potential control of these parasites.

Dr. Mikheyev next wants to turn these genomic tools toward new goals, such as identifying genes that help Varroa mites switch hosts. That type of information may help scientists give the western honey bee a leg up over a new scourge that — so far — just won’t let go.

This is a guest article from Kaylee Mueller, of Phase Genomics.

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