research on zebra mussels

Zebra Mussels: A guide to the good and the bad of these Great Lakes invaders

By Natasha Blakely

Zebra mussels are not native to the Great Lakes. They were first discovered in the area in the late 1980s, and it has been an ongoing battle to get rid of and control them ever since.

But what’s the issue? Mussels have long existed in the Great Lakes, and the dreissenid zebra mussels and native unionid mussels are both filter feeders.

The problem is that’s about where the similarities between the invasive and native species end.

For one thing, native mussels aren’t as efficient as zebra mussels, according to Diane Waller, a research fishery biologist with the U.S. Geological Survey. Waller studies zebra and quagga mussels at the USGS’s Upper Midwest Environmental Sciences Center .

A native mussel can take 3 to 5 years to mature, and they take a while to reproduce because they are parasitic.

Zebra mussels mature in a year and release their larvae into the water to develop.

The result is a storm of zebra mussels rapidly reproducing and spreading throughout the Great Lakes wherever the water takes them.

It’s an issue that has cost Canada and the United States separately billions of dollars.

But while many people know that zebra mussels are impacting the lakes, not many people know what that full range of impact is.

Here’s a list of those effects, both good and bad:

Coating pipes

One of the more well-known problems with zebra mussels is the way they rapidly coat water intake pipes, which is a problem for drinking water treatment plants, power plants and any other industry that’s pulling water out of the lakes through a pipe.

“Any facility that’s pulling water out of the Great Lakes has to deal with the potential for the mussel to be settling in their pipes and somewhere else in their system,” Waller said.

Sailing and shipping

Name an aspect of the boating or shipping industry, and zebra mussels are probably interfering in some way, whether it’s fouling up hulls, motors , docks or marinas.

Native mussels dying out

Freshwater mussels throughout the nation are already struggling , and it isn’t helping the situation when zebra mussels come in and take over their food and spawning grounds.

In many smaller inland lakes but also some areas of the Great Lakes where the invasive mussels have come in, native mussel species have been wiped out.

Harder for fish to spawn

Some Great Lakes fish spawn in reefs that contain piles of rocks and boulders, laying eggs in the crevices.

Zebra mussels have coated some of these reefs , resulting in the larvae not spawning well, affecting local fish populations, Waller said.

Dropping usage and values of beaches and beach property

Zebra mussel shells litter beaches and beachfront property around the Great Lakes, decreasing property values and the amount of beach use in those areas.

Changing research

The impact the mussels are having on research in the Great Lakes may not necessarily be bad, but there has been an undeniable effect.

At the Upper Midwest Environmental Science Center—the USGS research center Waller works at in La Crosse, Wisconsin—a chlorination plant was added to the facility once it started studying invasive species because of the risk involved in returning water to the lakes after it’s had contact with invasives.

“When you’re doing research, you have to follow all the prevention steps everyone else does and facilities are pulling water from all over the Great Lakes,” Waller said.

The way zebra mussels changed the Great Lakes ecosystems means the focus and base of knowledge for ecological and fisheries research has had to shift as well.

“We’ve had to reformulate our knowledge of things like nutrient cycles and trophic transfers and fisheries populations,” Waller said.

Cases of botulism

There appears to be a link between invasive zebra mussel populations and occurrences of botulism , according to Waller.

Botulism is a poisoning caused by toxins produced by Clostridium botulinum bacteria.

The theory is that the mussels filter out so much of the phytoplankton and suspended solids in the water that’s increased the growth of aquatic plants such as cladophora. When the cladophora dies and decays, it makes the water go low in oxygen, which could be what’s triggering the bacteria that causes botulism.

Changing food web

A water column is a conceptual column of water that runs from the surface of a lake to the lakebed.

With the zebra mussels coating lakebeds and filtering so much of the nutrients in the water column, a lot of energy is transferred to the bottom, which makes it more available for organisms living in the benthic—or bottom—zone of a water body.

Whether that’s a good or bad thing is up for debate.

“Initially we might say this particular species might benefit, but really I think we don’t yet know what some of those secondary effects might be even if it does look beneficial to a couple organisms,” Waller said.

Water clarity

Mussels are filter feeders, which means they feed by clearing nutrients from the water passing through them.

The rate of reproduction and spread of zebra mussels make them efficient cleaners of Great Lakes water, but whether that’s a positive or negative thing depends on who you’re asking.

“Some people do think the water clarity is a benefit,” Waller said. “I think that really depends. They can be accumulating like contaminants and bacteria that could be human pathogens, so it could be beneficial that they’re removing some of those, but then they also become a sink for it that could later be released.”

Featured Image: Invasive mussel shells among debris from the Detroit River (Photo Credit: Natasha Blakely)

• environment
• great lakes
• invasive species

About Natasha Blakely

10 comments.

What has been the real cost/benefit of the opening of the St. Lawrence Seaway? Should it have been kept closed to save the ecology of the lakes?

That’s a hard couple of questions to answer with a lot of different angles to address. The literal original cost of the St. Lawrence Seaway was $330 million for Canada and $130 million for the U.S. On a broader scale, it might have cost us the diversity and stability of the ecosystem back then. But the Great Lakes economy has evolved a lot with shipping, which may or may not be a good thing, depending on whom you ask. Playing the should-have game is even harder, especially when it comes to accurate reporting, because it’s hard to say what would have happened. It wasn’t kept closed, so what we have now is dealing with the consequences or the benefits of having the seaway. There are some books out there that cover the full history and impact of the seaway that you can check out for more information like “Pandora’s Locks: The Opening of the Great Lakes-St. Lawrence Seaway.”

– Natasha Blakely, Great Lakes Now news director

Is the mussel population increasing in Lake Erie. I work at an industrial site and it appears to us that since 2017 the population at the site has exploded. Appreciate any one’s input on this matter.

This is the perfect webpage for anyone who wishes to find out about this topic. You understand a whole lot its almost hard to argue with you (not that I really would want to…HaHa). You certainly put a fresh spin on a topic which has been discussed for ages. Great stuff, just great!

“Should it have been kept closed to save the ecology of the lakes?”

Such reasoning would not have survived WW2.

During the war, the lakes had something like a dozen shipyards churning out destroyers and transports. Being inland, they were immune to raiding and required no defenses.

Actually all of this a false, especially the patistitic part. this really made me upset because me being me,, a vegan, I hate watching people kill innocent species , let them live. I mean what would you do if your family was living their life the way they think is the right way to live, would you kill them too. you really need to get you facts straight. SAVE ALL ZEBRA MUSSELS!!!!!!!!!

stop the false news. zebra mussels are harming our environment it has nothing to do with you being a vegan

thank you for the article

Right on these are like little angels with calcified wings on a mission to clean the waters of all our environmental pollutants. Shame on those who intend to inhibit their glorious mission.

Every article I read about Zebra Mussels is gloom and doom about all of the negative effects and how fast they spread. Its been over 30 years since they were found in the US and I can’t find one article showing the actual damage they have done. Its all about what they can and will do. When exactly will we see all of this devastation? With no real damage being reported this seems more like a money grab than an actual problem.

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Zebra Mussels

Dreissena polymorpha.

Zebra mussels, though small, have huge impacts on our lakes. Their presence may greatly reduce lakefront property values and their sharp shells cut swimmer’s feet. Ecologically, they filter enormous quantities of microscopic algae and alter energy flow through aquatic ecosystems—impacting fish populations and smothering and causing extinctions of native mussels. Research at MAISRC focuses on finding effective and efficient ways to control them, establishing how they're spreading to better target prevention efforts, and informing management by developing early detection methods and creating survey protocols. More about zebra mussels .

MAISRC findings

• Completed sequencing of a draft genome of the zebra mussel in order to isolate markers to study spread and explore possible genetic weaknesses that can be targeted for control
• Identified where on a boat zebra mussels may be hiding to recommend decontamination techniques and watercraft redesign options
• Established how far zebra mussel larvae can spread down small rivers and streams. Research showed that settlement of mussels occurs only a short distance down from the upstream lake. Small streams can carry large numbers of larvae, but only down short (<10 miles) stretches of streams
• Identified the lowest effective dilution of antifreeze and the shortest period of contact time required to effectively kill zebra mussels during boat winterization
• Established best practices for using EarthTec QZ, a commercially available molluscicide, to control populations by suppressing veligers
• Developed rapid response toolkit to treat localized zebra mussel infestations based on water temperature and size of infestation. The protocols provide managers with a critical support tool to swiftly select the correct molluscicide, determine the treatment concentration, and determine the treatment duration
• Developed an early detection tool that simultaneously detects the presence of zebra mussels, quagga mussels, and their microscopic larvae with just one lake water sample

RNA-interference screens for zebra mussel biocontrol target genes

This project will develop methods of RNA-interference (RNAi) to identify genetic weak points in zebra mussels and to develop the tools to manipulate these critical genes as a stepping-stone towards targeted genetic biocontrol efforts.

Led by Dr. Daryl Gohl

Copper-based control: zebra mussel settlement and nontarget impacts

Researchers will use a biotic ligand model (BLM) to predict the lake-specific minimum toxic copper concentration to target zebra mussel veligers.

Led by Dr. Diane Waller

Evaluating innovative coatings to suppress priority AIS

This project will develop and test a non-toxic, new coating that can mitigate the spread of zebra mussels while minimizing non-target impacts. 

Led by Dr. Mikael Elias

Public values of aquatic invasive species management

This project looks to to quantify and analyze the ecological and economic value of AIS damages and AIS management as they relate to ecosystem services such as fishing, swimming, biodiversity, and navigability. 

Led by Dr. Amit Pradhananga

Early detection of zebra mussels using multibeam sonar

This study will test the utility of swath mapping systems such as multibeam sonar for detecting and quantifying the abundance of invasive mussels at a very large scale.

Led by Dr. Jessica Kozarek

A novel technology for eDNA collection and concentration

Researchers developed an eDNA filter that can screen quickly and cost-efficiently for native, invasive, and endangered species. 

Led by Dr. Abbas Abdennour

Sustaining walleye populations: assessing impacts of AIS

The overall goal of this project is to assess the impacts of invasive zebra mussels and spiny water fleas on walleye in Minnesota lakes. 

Led by Dr. Gretchen Hansen

Temperature-dependent toxicity of molluscicides to zebra mussels

This project created water-temperature dependent treatment protocols to eradicate localized zebra mussel infestations in a rapid response scenario.

Led by Dr. James Luoma

Decision-making tool for optimal management of AIS

This project will develop a decision-making tool to help AIS managers, counties, and other agencies prioritize their resources for optimal prevention and intervention of AIS, specifically zebra mussels and starry stonewort. 

Led by Dr. Nicholas Phelps

Cost-effective monitoring of lakes newly infested with zebra mussels

This project will develop recommendations for underwater survey methods to estimate zebra mussel population abundance and distribution.

Led by Dr. John Fieberg

Metagenomic approaches to develop biological control strategies for aquatic invasive species

This project will identify and isolate microbes that are potentially pathogenic to AIS, and evaluate the specificity and effectiveness of potential biocontrol agents in the laboratory.

Led by Dr. Michael Sadowsky

Estimating overland transport frequencies of invasive zebra mussels

This study aimed to estimate the relative contributions of different surfaces and compartments on and in recreational boats and trailers to the transport of zebra mussels and their larvae (veligers), focused on measurements of the concentrations of veligers in residual water across a full range of vessel types in Minnesota.

Led by Dr. Mike McCartney

Evaluating boat cleaning station efficacy on the removal of residual water from recreational boats

This study evaluated the practicality and effectiveness of a CD3 Cleaning Station vacuum for removing residual water from various recreational boats.

Zebra, quagga, and native mussel research efforts on the St. Croix Scenic Riverway and Apostle Islands National Lakeshore

At the St. Croix National Scenic Riverway, researchers collected zebra mussel veliger samples from throughout the riverway and analyzed them to determine population and reproduction dynamics.

Led by Dr. Michael McCartney

Genome sequencing and analysis to select target genes and strategies for genetic biocontrol

This project mapped and shared a publicly accessible genome of the zebra mussel: a powerful tool for invasion biology and biocontrol researchers in Minnesota and worldwide.

Toxicity of antifreeze to zebra and quagga mussels

The goal of this project was to identify the lowest effective dilution of antifreeze at the shortest period of contact time to effectively kill adult and juvenile quagga mussels and juvenile zebra mussels.

Recognizing high-risk areas for zebra mussels and Eurasian watermilfoil invasions in Minnesota

The goal of this project was to improve the decision-making process and prevent the spread of AIS by implementing risk-based prevention and mitigation management strategies.

Developing and testing a new molecular assay for early detection of zebra mussel veligers

This project developed an early detection molecular assay for detecting and quantifying zebra and quagga mussel DNA in environmental mixtures of the two species. 

Creation of survey and monitoring protocols, and development of a research program for studying the effectiveness of zebra mussel pesticide treatment efforts

In partnership with the Minnesota DNR Invasive Species program, MAISRC provided a description of the Pilot Project Program and the application process to obtain a permit for treating newly infested lakes.

Evaluating zebra mussel spread pathways and mechanisms in order to prevent further spread

This project focused on preventing zebra mussel invasions by developing genetic evidence of spread sources and pathways so that they may be interrupted. It also lays the groundwork for potential biocontrol through genetic modification technologies.

Eco-epidemiological model to assess aquatic invasive species management

MAISRC researchers are working to develop a first-of-its-kind eco-epidemiological model that will forecast the potential risk of spread of zebra mussels and starry stonewort across Minnesota. 

About zebra mussels

+ description.

Zebra mussels are ¼-1 ½ inch-long bivalve (2-shelled) molluscs. They evolved from ancestors similar to surf clams (used to make clam chowder) that invaded fresh waters in southern Russia. They have a D- or wedge-shaped shell, which is often marked by alternating brown and yellow bands in a zigzag pattern. They live on lake and river bottoms, rocks, aquatic plants, docks, lifts, and boats to which they attach using small dark fibers called "byssal threads." Viewed up-close underwater, two tiny siphons can be seen projecting into a narrow gap between the shell valves of each animal — these siphons are used to pump water for respiration and feeding.

+ Life cycle

Zebra mussels cause economic harm in North America of over one billion dollars per year. Their huge populations attach to hard surfaces, clog intake pipes for water treatment and power generating plants, encrust boat motors and hulls, may greatly reduce lakefront property values, and their sharp shells cut swimmer’s feet. Ecologically, they filter enormous quantities of microscopic algae and alter energy flow through aquatic ecosystems — with potentially large impacts on fish populations — and they smother and cause extinctions of native bivalve mollusks. 

+ Distribution

Zebra mussels are native to large rivers and lakes draining into the Black, Caspian, and Azov Seas of southwestern Russia and the Ukraine. Beginning in about 1800, they began spreading across western and northern Europe and most recently have reached inland waters in the British Isles, Spain, Portugal, and France. They appeared in North America in 1988, and in five years they spread rapidly throughout the Great Lakes and large rivers. In several Great Lakes (particularly Michigan and Erie) zebra mussels have been largely replaced by a related species — the quagga mussel ( D. bugensis ) — also from the Black Sea. Zebra mussels arrived in the Duluth Harbor in 1989 and the Mississippi River in 1993. As of May 2018, the Minnesota Department of Natural Resources listed 335 waterbodies in the state as infested due to either confirmed zebra mussel presence or connection to a waterbody with a confirmed presence.

+ How they spread

In the 19th century, zebra mussels spread throughout Europe in man-made canals, and in the late 20th century, on recreational watercraft and the nets of commercial fisherman. They were also spread to lakes in Poland and Belarus on the nets of commercial fisherman. In North America, barge traffic and (to unknown extent) larval dispersal were responsible for rapid initial spread throughout the Great Lakes, Mississippi, Ohio and Susquehanna Rivers. Spread to inland lakes has occurred by larvae transported down connected streams and waterways, and overland via mussels attached to vegetation and to surfaces of recreational boats, trailers, docks and lifts. Veliger larvae may also be transported in the "residual water" remaining inside boat compartments when trailered boats are moved between waterways.

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Invasive zebra mussels.

Prevention is the best way to keep a water body clean of zebra mussels. Sophie Koch

NPS / Schaeppi

“Biofouling,” or the accumulation of adult zebra mussels on surfaces put in the water, is one of the more notable impacts zebra mussels can have on a local economy. Zebra mussels are armed with rootlike threads of protein, called “byssal threads,” that allow them to firmly attach themselves to hard surfaces such as rocks, native mussels, docks or boats. Typically, this isn’t a problem for boats that are only in the water for short trips, but boats, docks or intake pipes that are left in the water for a long period of time can become encrusted and be very difficult to clean. If a boat owner also fails to drain the water from his or her motor, any veligers floating in the water will root themselves and clog the machinery as they reach adulthood.

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Last updated: April 2, 2021

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• Aquatic Invasives
• Aquatic Invertebrates

Zebra Mussel

Dreissena polymorpha (Pallas, 1771) ( ITIS )

Zebra mussel

Eurasia ( NAS Database )

1988 ( NAS Database )

Ballast water ( NAS Database )

Competes with native species; clogs pipes ( NAS Database )

Zebra mussel, adult

Photo by Amy Benson; U.S. Geological Survey

Find more images

• Google Images - Zebra Mussel
• Invasive.org - Zebra Mussel
• Nonindigenous Aquatic Species Database - Zebra Mussel Images

CPW (Colorado Parks & Wildlife) Provides Update on the Discovery of Zebra Mussel Veligers in the Colorado River and Government Highline Canal

• Jul 26, 2024

Colorado Parks & Wildlife.

Colorado Parks and Wildlife (CPW) announces additional zebra mussel veligers found in the Colorado River and Government Highline Canal after increased testing. With these additional detections, both the Highline Government Canal and the Colorado River meet the criteria for being considered “positive” for zebra mussels. See also: Colorado Parks and Wildlife announced discovery of zebra mussels in the Colorado River and the Government Highline Canal (July 16, 2024), nearly two years after the invasive species was first detected in the state. 

Invasive Zebra Mussels Detected on Aquarium Marimo Moss Balls

• Aug 8, 2024

Washington Department of Fish and Wildlife.

On August 5, the Washington Department of Fish and Wildlife (WDFW) received notification from a local wholesale aquarium company in Renton of possible invasive freshwater mussels on a shipment of Marimo moss balls ( Aegagropila linnaei ). Moss balls are a commonly used decorative algae in aquariums and water gardens. Lab testing confirmed the mussels were zebra mussels ( Dreisena polymorpha ), a prohibited aquatic invasive species in Washington that, if established in local waters, would be capable of causing significant infrastructure and environmental damage. Zebra mussels and a close relative, the quagga mussel, are not known to be established in Washington.

Mussel-Fouled Boat Intercepted at Anaconda Inspection Station

• Mar 12, 2024

Montana Fish, Wildlife & Parks.

Montana’s first mussel-fouled watercraft of the year was intercepted at the Anaconda watercraft inspection station on March 10.

All watercraft entering the state of Montana with the intent of being launched into any body of water are required to be inspected, including kayaks, canoes, rafts and paddleboards. These inspections are required by law, and failure to comply may result in a fine of up to $500. Learn more how Protect Montana Waters from Aquatic Invasive Species .

Army Corps of Engineers: Better Data and Planning Needed to Combat Aquatic Invasive Species

• Nov 6, 2023

United States Government Accountability Office.

Quagga and zebra mussels have spread rapidly across the country since they were first discovered in the late 1980s and, according to U.S. Army Corps of Engineers officials, have spread to every major river basin in the U.S. except the Columbia River Basin in the northwest. The mussels typically are spread by recreational watercraft such as boats, canoes, and Jet Skis that have been in infested waters. Once established in a water body, the mussel species are extremely difficult to eradicate because they have no natural predators in the U.S. and rapidly reproduce.

GAO was asked to examine efforts the Corps has undertaken to prevent the spread of aquatic invasive species into the Columbia River Basin by recreational watercrafts. This report [PDF, 3.24 MB] provides information on the Corps' Watercraft Inspection and Decontamination Program and its role in helping to prevent the introduction or spread of quagga and zebra mussels—the aquatic invasive species of greatest concern to the Corps—as well as program challenges and opportunities for improvement.

Invasive Zebra Mussels Now Confirmed in North Carolina

• Sep 22, 2023

North Carolina Wildlife Resources Commission.

The North Carolina Wildlife Resources Commission (NCWRC) announced today that zebra mussels , a harmful invasive aquatic species, have been identified in an Iredell County waterbody. This is the first time this species has been identified in the wild in North Carolina. On Thursday, September 21, 2023, NCWRC , with assistance from scuba divers from the U.S. Fish and Wildlife Service, investigated and confirmed a report of zebra mussels in a quarry on private property. NCWRC believes the mussels are contained to the quarry and is working on options for treatment while continuing its investigation.

To report suspected zebra mussels, please contact the NCWRC 's district fisheries biologist offices . Visit NCWRC 's aquatic nuisance species webpage for guidance on disinfecting snorkel and SCUBA gear and for more information on zebra mussels.

Zebra Mussels Found in Aquarium Moss Balls

Invasive zebra mussels have been found in "moss balls” an aquarium plant product sold at aquarium and pet supply stores.  Zebra mussels are regarded as one of the most destructive invasive species in North America. Learn more about the situation, rapid response efforts by federal and state agencies, and how to properly destroy the moss balls to prevent the spread of zebra mussels.

Updated Recommendations for the Quagga and Zebra Mussel Action Plan for Western U.S. Waters [PDF, 3.93 MB]

Western Regional Panel on Aquatic Nuisance Species.

The Western Regional Panel prepared Quagga and Zebra Mussel Action Plan 2.0 to inform ongoing management and partnership efforts intended to minimize the spread and impacts from zebra and quagga mussels in the western United States. The original QZAP action items have guided prevention, containment, research, and management to address the ecological and economic impacts of invasive quagga and zebra mussels since 2009. The purpose of QZAP 2.0 is to provide a systematic and unified approach to prevent the spread of zebra and quagga mussels into and within the western United States in the future. The urgency and the need for such a coordinated approach remain as important today as ever before. Newly infested waters, increased boating pressure, and gained public and political awareness drove the need for the Western Regional Panel to acknowledge and learn from the past and set forth a new collective path towards the future. These recommendations are intended to inform decision-making to provide increased capacity and clear direction that empowers the further implementation of a collaborative and coordinated multi-jurisdictional regional strategy to prevent the spread of quagga and zebra mussels in the West. For more resources, see: Key Documents

Invasive Mussels in the American West

DOI . United States Geological Survey.

A geonarrative by USGS and Geoplatform.gov examining the spread of invasive mussels in the American West.

See also: Geonarratives for all USGS geonarrative / story map resources

Distribution / Maps / Survey Status

Nonindigenous aquatic species database: point map - zebra mussel.

DOI . USGS . Wetland and Aquatic Research Center.

Provides detailed collection information as well as animated map.

Federally Regulated

Injurious wildlife listings - keeping risky wildlife species out of the united states.

DOI . FWS . Fish and Aquatic Conservation.

Includes species listed as injurious wildlife under the Federal Lacey Act ( 18 USC 42 ), which makes it illegal to import injurious wildlife into the U.S. or transport between the listed jurisdictions in the shipment clause (the continental U.S., the District of Columbia, Hawaii, the Commonwealth of Puerto Rico, and any possession of the U.S.) without a permit. An injurious wildlife listing would not prohibit intrastate transport or possession of that species within a State where those activities are not prohibited by the State. Preventing the introduction of new harmful species is the only way to fully avoid impacts of injurious species on local, regional, and national economies and infrastructure, and on the natural resources of the U.S.

Injurious wildlife are wild mammals, wild birds, amphibians, reptiles, fishes, crustaceans, mollusks and their offspring or eggs that are injurious to the interests of human beings, agriculture, horticulture, forestry, wildlife or wildlife resources of the U.S. Plants and organisms other than those stated above cannot be listed as injurious wildlife. For more information, see What Are Injurious Wildlife: A Summary of the Injurious Provisions of the Lacey Act and Summary of Species Currently Listed as Injurious Wildlife .

YouTube - Stop Zebra Mussels

Google. YouTube; Texas Parks and Wildlife.

All Resources

Selected resources.

The section below contains highly relevant resources for this species, organized by source.

Fact Sheet: Zebra Mussel | Quagga Mussel [PDF, 500 KB]

Alberta Invasive Species Council (Canada).

See also: Fact Sheets for more information about individual invasive species, including those listed as "Prohibited Noxious" and "Noxious" under the Alberta Weed Control Act

Priority Species: Zebra and Quagga Mussels

Washington State Recreation and Conservation Office. Washington Invasive Species Council.

NOBANIS: Invasive Alien Species Fact Sheet - Dreissena polymorpha [PDF, 217 KB]

European Network on Invasive Alien Species.

See also: NOBANIS Fact Sheets for invasive alien species of the European region, covering both animals and plants, as well as microorganisms

Global Invasive Species Database - Dreissena polymorpha (mollusc)

IUCN . Species Survival Commission. Invasive Species Specialist Group.

Invaders Factsheet: Zebra and Quagga Mussel

Ontario's Invading Species Awareness Program (Canada).

Invasive Mussel Collaborative

DOI . U.S. Geological Survey; Great Lakes Commission; DOC . National Oceanic and Atmospheric Administration; Great Lakes Fishery Commission.

Invasive Species Compendium - Dreissena polymorpha

CAB International.

NEANS Panel Online Guide - Zebra Mussel

Northeast Aquatic Nuisance Species Panel.

Non-native Species Information: Zebra Mussel

Great Britain Non-Native Species Secretariat.

Texas Invasives Database - Dreissena polymorpha

TexasInvasives.org.

The Quiet Invasion: A Guide to Invasive Species of the Galveston Bay Area - Zebra Mussel; Quagga Mussel

Texas Commission on Environmental Quality, Galveston Bay Estuary Program; Houston Advanced Research Center (HARC).

National Exotic Marine and Estuarine Species Information System (NEMESIS) - Dreissena polymorpha

Smithsonian Institution. Smithsonian Environmental Research Center. Marine Invasions Research Lab.

Nonindigenous Aquatic Species Database: Fact Sheet - Zebra Mussel

Provides distribution maps and collection information (State and County).

Quagga and Zebra Mussels

DOI . Bureau of Reclamation. 

Environmental Fact Sheet: Zebra Mussels [PDF, 673 KB]

New Hampshire Department of Environmental Services.

See also: Publications - Invasive for more resources

Preventing Freshwater Aquatic Invasive Species: Zebra Mussel [PDF, 1.2 MB]

Rhode Island Department of Environmental Management. Office of Water Resources.

See also: Aquatic Invasive Animals for species of concern

Aquatic Nuisance Species List - Zebra Mussels

Kansas Department of Wildlife, Parks, and Tourism.

Field Guide: Invasive - Zebra Mussel

Missouri Department of Conservation.

See also: Zebra Mussel Control

Invasive Concerns: Zebra & Quagga Mussels

See also: Highline Lake - Zebra Mussel Information

Invasive Species Information: Zebra Mussel

Massachusetts Department of Conservation and Recreation.

Maryland Invasive and Exotic Species - Zebra Mussels

Maryland Department of Natural Resources.

California Department of Fish and Game.

Wisconsin Department of Natural Resources.

Zebra Mussels

Virginia Department of Wildlife Resources.

Utah Pests Fact Sheet - Quagga Mussel and Zebra Mussel [PDF, 1.83 MB]

Utah State University Extension; Utah Plant Pest Diagnostic Laboratory.

See also: Invasive Species for more fact sheets

Aquatic Invasive Species in the Chesapeake Bay - Zebra Mussels [PDF, 127 KB]

Maryland Sea Grant.

See also: Six Species of Concern for more fact sheets

Zebra Mussels Pose a Threat to Virginia's Waters

Virginia Tech; Virginia State University. Virginia Cooperative Extension.

AIS in Minnesota - Zebra Mussels

University of Minnesota. Minnesota Aquatic Invasive Species Research Center.

Factsheet: Zebra Mussel and Quagga Mussel

Pennsylvania State University. Pennsylvania Sea Grant.

See also: Aquatic Invasive Species Fact Sheets for additional species information

Introduced Species Summary Project - Zebra Mussel

Columbia University. Center for Environmental Research and Conservation.

Invasive Species Information: Zebra/Quagga Mussel

Paul Smith's College (New York). Adirondack Watershed Institute.

Quagga & Zebra Mussels

University of California - Riverside. Center for Invasive Species Research.

Zebra Mussels and Quagga Mussels

Tip of the Mitt Watershed Council (Michigan).

Integrated Taxonomic Information System. Dreissena polymorpha . [Accessed Sep 30, 2023].

Nonindigenous Aquatic Species Database. Fact Sheet - Zebra Mussel . USGS , Gainesville, FL . [Accessed Sep 30, 2023].

Center for Invasive Species Research

DEPARTMENT OF ENTOMOLOGY

Quagga & Zebra Mussels

Quagga  dreissena rostriformis bugensis and zebra  dreissena polymorpha  mussels.

The Situation:  Quagga and zebra mussels are aquatic invasive species that are native to eastern Europe. The quagga mussel originated from Dnieper River drainage of Ukraine. The zebra mussel was first described from the lakes of southeast Russia and its natural distribution also includes the Black and Caspian Seas. Quagga and zebra mussels get their common names from the zebra-type striping on the shells. Both mussel species are small and typically grow to the size of a fingernail. They are prolific breeders and these mussels can attach to both hard and soft surfaces in freshwater ways.

Zebra mussels have a long history of invasion and have successfully established in Great Britain (1824), The Netherlands (1827), The Czech Republic (1893), Sweden (1920), Italy (1973), the Great Lakes in the USA (1988), and California (2008). Quagga mussels were first found in the USA in the Great Lakes in 1989, Nevada in 2007, and California in 2008. Ballast water discharge from transoceanic ships is thought to be responsible for the long distance spread of zebra and quagga mussels from their original home ranges in eastern Europe. Short distance spread between fresh waterways within countries most likely occurs via the movement of recreational boats. This occurs when boats are not cleaned and dried adequately and contaminated watercraft are then moved from infested waterways to pristine water bodies where mussels are accidentally introduced. These mussels can survive for 3-5 days out of water without suffering lethal desiccation.

Where quagga and zebra mussels co-exist, quagga mussels appear to outcompete zebra mussels, and quagga mussels can colonize to depths greater than those achieved by zebra mussels and are more tolerant of colder water temperatures. For example, in Lake Michigan, zebra mussels made up 98.3% of mussels in 2000, by 2005 quagga mussels represented 97.7% of collected mussels. Zebra mussels were found at densities of around 899 per square meter, but quagga mussels now dominate at 7,790 mussels per square meter. Quagga mussels have been found at depths of up to 540 feet in Lake Michigan where they filter feed year round.Consequently, quagga mussels may end up being the more problematic of these two mussel species in California. The Problem:  Quagga and zebra mussel invasions have had catastrophic impacts in the ecosystems in which they have established. These organisms clog water intake structures (e.g., pipes and screens), which greatly increases maintenance costs for water treatment and power plants. Recreational activities on lakes and rivers are adversely affected as mussels accumulate on docks, buoys, boat hulls, anchors, and beaches can become heavily encrusted.

The shells of both mussel species are sharp and can cut people, which forces the wearing of shoes when walking along infested beaches or over rocks. Mussels adhering to boat hulls can increase drag, affect boat steering, and clog engines, all of which can lead to overheating and engine malfunctions. Ecological problems also result from mussel invasions. Zebra and quagga mussels can kill native freshwater mussels in two ways: (1) attachment to the shells of native species can kill them, and (2) these invasive species can outcompete native mussels and other filter feeding invertebrates for food. This problem has been particularly acute in some areas of the USA that have a very rich diversity of native freshwater mussel species.

The encrusting of lake and river bottoms can displace native aquatic arthropods that need soft sediments for burrowing. In the Great Lakes this had lead to the collapse of amphipod populations that fish rely on for food and the health of fish populations has been severely affected.

These mussels have been associated with avian botulism outbreaks in the Great Lakes which have caused the mortality of tens of thousands of birds. Because of their filter feeding habit, it has been estimated that these mussels can bioaccumlate organic pollutants in their tissues by as much as 300,000 times when compared to concentrations in the water in which they are living. Consequently, these pollutants can biomagnify as they are passed up the food chain when contaminated mussels are eaten by predators (e.g., fish and crayfish), who in turn are eaten by other organisms (e.g., recreational fishermen who eat contaminated fish.) High mussel populations can increase water acidity and decrease concentrations of dissolved oxygen.

Interestingly, invasions by quagga and zebra mussels have been documented as having some positive affects on receiving ecosystems. For example, filtration of water by mussels as they extract food removes particulate matter. This filtration has improved water clarity, and reduced the eutrophication of polluted lakes. In some instances these improvements may have benefited local fishing industries. Conversely, improved water clarity allows penetration of light to greater depths which can alter the species composition of aquatic plant communities and associated ecosystems. This improved water quality is thought to aid algal blooms that get washed ashore where they rot making recreational beaches unusable. Further, the highly efficient removal of phytoplankton can deprive other aquatic species of food.

 Invasion success in some areas of California may be affected by water chemistry. Waterways around the Sierra Nevada mountains may have insufficient calcium (an element needed for shell growth) and some lakes in northeast California may be too salty for mussel survival. However, the general consensus is that most freshwater ways in California will be accommodating to zebra and quagga mussels.

Economic Impact and Management:  Zebra and quagga mussel invasions create an immense financial burden because of the need to continuously and actively manage these pests. It has been estimated that it costs over $500 million (US) per year to manage mussels at power plants, water systems, and industrial complexes, and on boats and docks in the Great Lakes. Similar yearly management costs are anticipated for California. For example, a recent estimate (2009) by the Army Corps of Engineers indicates that quagga mussels could cause annual loses of $22 million to the Lake Tahoe region should they establish there. The report details potential damage to tourism, reduced property values, and increased maintenance costs. Management of problematic mussel populations may be achieved in different ways in California. Water draw downs in canals and aqueducts could be used to kill mussels by drying them out. Poisons such as chlorine and copper sulfate which are toxic to quagga and zebra mussels could be employed under certain conditions.

Center for Invasive Species Research, University of California Riverside 

Text and provided by:  Mark S. Hoddle,  Department of Entomology, University of California, Riverside Photos courtesy of the California Department of Fish and Game. Photo illustration courtesy of the US Geological Survey. 

Mark Hoddle , Extension Specialist and Director of Center for Invasive Species Research [email protected]  Personal Website

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What are zebra mussels and why should we care about them?

Zebra mussels are an invasive, fingernail-sized mollusk that is native to fresh waters in Eurasia. Their name comes from the dark, zig-zagged stripes on each shell.

Zebra mussels probably arrived in the Great Lakes in the 1980s via ballast water that was discharged by large ships from Europe. They have spread rapidly throughout the Great Lakes region and into the large rivers of the eastern Mississippi drainage. They have also been found in Texas, Colorado, Utah, Nevada, and California.

Zebra mussels negatively impact ecosystems in many ways. They filter out algae that native species need for food and they attach to--and incapacitate--native mussels. Power plants must also spend millions of dollars removing zebra mussels from clogged water intakes.

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Zebra Mussel, Lake Huron specimens.

Zebra Mussel

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Zebra Mussels: What You Should Know About This Invasive Species

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Zebra mussels are small freshwater shellfish named for the contrasting stripes that decorate their shells. Native to the lakes and rivers that drain into the Caspian, Azov, and Black seas in eastern Europe and western Asia, these mussels are now widespread throughout Europe and the United States, usually traveling into new waterways attached to boats, as well as via water discharged from large ships (called ballast water).

Growing to be about an inch in size, each female zebra mussel can produce up to 1 million microscopic larvae, and the mollusks have spread rapidly across the eastern United States since their introduction in the 1980s, causing hundreds of millions of dollars in economic damage and altering ecosystems dramatically.

Zebra mussels are unique when compared to native freshwater bivalves in that they have byssal threads — strong, silky fibers, also called beards, that they use to attach to objects and remain stationary. Byssal threads allow zebra mussels to cover and incapacitate larger native mussel species, and also to accumulate on the surface of the shallow water, as well as inside pipes and all types of equipment, clogging them as more and more mussels grow inside. These mussels also have a unique reproduction capacity, releasing free-swimming larvae called veligers. Zebra mussels are an invasive species , and it is illegal to knowingly possess or transport them in the United States.

How Were Zebra Mussels Introduced to the United States?

Zebra mussels ( Dreissena polymorpha) are a native of the Ponto-Caspian region, and began spreading across Europe along trade routes in the 1700s. It wasn't until the latter part of the 20th century that zebra mussels established a population in the United States. Researchers are not sure exactly when these mussels first arrived, but it is believed to have been in the mid to late 1980s, when a transatlantic cargo ship (or several) released ballast water containing zebra mussel larvae into the Great Lakes.

This mussel is unique compared to other freshwater bivalves, except perhaps Mytilopsis, because it produces veligers. It is often during this life phase that the species colonizes new environments, though zebra mussels can disperse during all life stages. Veligers are microscopic, and recreational boaters catching bait fish, swimming, and moving their vessels between different rivers and lakes, also began transferring zebra mussels into other parts of the Great Lakes system after their initial introduction.

Eventually, they were present in most navigable waterways in the eastern United States, crossing 23 states in around 15 years. While there is an established population of zebra mussels in the Colorado River and its tributaries, the bulk of the western states have yet to see an explosion of zebra mussels. The threat of their economic and environmental impact has led some states to take preventive actions, working to raise public awareness an invest in watercraft inspections and decontaminations to stop the mussel's spread.

Like many invasive species with a rapidly expanding population, zebra mussels have several characteristics that distinguish them from native freshwater mussels and allow them to exploit an "empty niche" in North American freshwater ecosystems. They reproduce prolifically, and their larvae require several weeks of development, during which they can be widely dispersed by winds and currents. Their byssal threads are also an advantage, allowing them to attach to mussels and other surfaces. Their ability to rapidly consume primarily phytoplankton, which serves as an important part of the food chain, also helps them thrive.

Problems Caused By Zebra Mussels

Alteration of food webs.

Zebra mussels form dense mats that can filter massive amounts of water. In parts of the Hudson River, their densities can reach over 100,000 individual mussels per square meter, and they are capable of filtering all of the water in the freshwater portion of the river every two to four days. Before zebra mussels arrived in the Hudson, native mussels filtered the water every two to three months. The phytoplankton, small zooplankton, large bacteria, and organic detritus that zebra mussels eat as they filter the water, straining out the edible material, form the base of the aquatic food web, leading scientists to fear cascading effects throughout the food chain as reductions of plankton in the biomass may cause increased competition, decreased survival, and decreased biomass of fish that also rely on the tiny organisms for food.

Biofouling occurs when organisms accumulate in unwanted areas, commonly seen with barnacles and algae. Zebra mussels colonize pipes at hydroelectric and nuclear power plants, public water supply plants, and industrial facilities, constricting flow and reducing the intake in heat exchangers, condensers, fire fighting equipment, and air conditioning and cooling systems. They also negatively impact navigational and recreational boating, increasing drag due to attached mussels. Small mussels can get into engine cooling systems, causing overheating and damage, and navigational buoys have been sunk under the weight of attached zebra mussels. Long-term attachment of these mussels also causes corrosion of steel and concrete as well as deterioration of dock pilings.

Zebra mussels will form large exposed mats on shorelines and in shallow water, decreasing opportunities for recreation in those areas, as beach-goers need protective shoes to avoid being cut by the shells. In a survey of power and water companies across the mussel's range, over 37% of surveyed facilities reported finding zebra mussels and 45% had initiated preventive measures to keep zebra mussels from entering the facility operations. Almost all surveyed facilities with zebra mussels had used control or mitigation alternatives to remove or control zebra mussels, with an estimated 36% of surveyed facilities experiencing an economic impact, estimated at $267 million total.

Harm to Native Species of Mussels

Jennifer Idol / Getty Images

Zebra mussels harm native mussel species in many ways, including attaching via their beards and impeding valve operation, causing shell deformity, smothering siphons (long tubes that exchange water and air), competing for food, impairing movement, and depositing metabolic waste.

According to research by the U.S. Geological Survey, survival rates of native unionid (a family of freshwater mussels) in the Mississippi River in Minnesota have been shown to decline significantly with an increase in zebra mussel colonization, and unionidae have been completely eliminated from Lake St. Clair and almost extirpated in western Lake Erie.

Efforts to Curb Environmental Damage

Because zebra mussels reproduce prolifically and their larvae are microscopic, it's difficult to eradicate an established population, leading most officials to encourage the general public to be educated about how zebra mussels can spread and how to stop that from happening. Zebra mussels can easily be accidentally transferred from water in bait buckets, or attached to different parts of boats, meaning that carefully cleaning boats, trailers, and gear, can help a lot to reduce their movement.

In recent years, scientists have been working to sequence the genome of this mussel, in the hopes that a chemical or biological tool can be developed to specifically target and kill this species without harming other organisms. As it stands, there are a variety of poisons that officials have used to kill the mussels with varying degrees of success, but of course any poison released into the water could also have an impact on other species present.

Perhaps the most interesting (and ironic) development in zebra mussel-infested waterways has been the arrival of the quagga musse l ( Dreissena bugensis ), an invasive cousin of the zebra mussel that has displaced the earlier-arriving species in some shallow waterways. Zebra mussels continue to dominate in faster-moving waterways, something researchers are tentatively attributing to a stronger byssal thread attachment . New management strategies are looking at solutions for both of these invasive species and hoping to stop further damage to aquatic ecosystems and water infrastructure.

Vanderbush, Brandon, et al. " A Review of Zebra Mussel Biology, Distribution, Aquatic Impacts, and Control with Specific Emphasis on South Dakota, USA ." Open Journal of Ecology , vol. 11, no. 2, 2021, doi:10.4236/oje.2021.112014 

" Zebra and Quagga Mussel ." New York Invasive Species Information .

Vanni, Michael. " Invasive Mussels Regulate Nutrient Cycling in the Largest Freshwater Ecosystem on Earth ." PNAS , vol. 118, no. 8, 2021, pp. e2100275118, doi:10.1073/pnas.2100275118

" Zebra Mussel ( Dreissena polymorpha ) ." United States Geological Survey .

Travina, Oksana, et al. " Molecular Data on  Phyllodistomum macrocotyle  (Digenea: Gorgoderidae) from an Intermediate Host  Dreissena polymorpha  (Bivalvia: Dreissenidae) in the Northern Dvina River Basin, Northwest Russia ." Ecologica Montenegrina , vol. 39, 2021, doi:10.37828/em.2021.39.7

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The genome of the zebra mussel, Dreissena polymorpha : a resource for comparative genomics, invasion genetics, and biocontrol

Michael a mccartney.

1 Department of Fisheries, Wildlife and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, St. Paul, MN 55108, USA

Benjamin Auch

2 University of Minnesota Genomics Center, Minneapolis, MN 55455, USA

Thomas Kono

3 Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA

Sophie Mallez

Angelico obille.

4 Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada

Aaron Becker

Juan e abrahante.

5 University of Minnesota Informatics Institute, Minneapolis, MN 55455, USA

Jonathan P Badalamenti

Adam herman, hayley mangelson.

6 Phase Genomics, Seattle, WA 98109, USA

Ivan Liachko

Shawn sullivan.

7 Department of Materials Science & Engineering, University of Toronto, Toronto, ON M5S 3E4 Canada

8 Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada

Sergey Koren

9 Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA

Kevin A T Silverstein

Kenneth b beckman, daryl m gohl.

10 Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA

Associated Data

The D. polymorpha genome assembly is available at NCBI (BioProject: PRJNA533175). Sequencing data files are available through the NCBI Sequence Read Archive (BioProject: PRJNA533175, PRJNA533176). This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAIWYP000000000 . The version described in this paper is version JAIWYP010000000 .

Supplementary material is available at G3 online.

Zebra mussels are one of the world’s most damaging invasive species. Native to Eurasia, they have continued to spread rapidly though Europe and in recent decades through North America, causing billions of dollars in economic damage and dramatically altering the ecosystems of infested lakes and rivers. Here we report the sequencing of the zebra mussel genome which will be an important tool for invasive species research and biocontrol efforts.

The zebra mussel, Dreissena polymorpha , continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate a high-quality chromosome-scale genome assembly. Through comparative analysis and transcriptomics experiments, we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact steamer-like elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.

Introduction

Native to a small region of southern Russia and Ukraine ( Stepien et al. 2014 ), zebra mussels ( Dreissena polymorpha , Figure 1A ) have spread throughout European ( Karatayev et al. 1997 , 2003 ) and North American ( Benson 2014 ) fresh waters to become one of the world’s most prevalent and damaging aquatic invasive species ( Karatayev et al. 2007 ). Fouling of water intake pipes cost the power generation industry over $3 billion USD from 1993 to 1999 in the Laurentian Great Lakes region alone ( O’Neill Jr. 2008 ), where Dreissena cause extensive damage to hydropower, recreation and tourism industries, and lakefront property ( Bossenbroek et al. 2009 ; Limburg et al. 2010 ). Dense infestations smother and outcompete native benthic species and remove large amounts of phytoplankton from lakes and rivers, causing population declines and extinctions of native freshwater mussels and other invertebrates, damage to fish populations ( Raikow 2004 ; Strayer et al. 2004 ; McNickle et al. 2006 ; Karatayev et al. 2014 ; Lucy et al. 2014 ; Ward and Ricciardi 2014 ), and dramatic restructuring of aquatic food webs ( Higgins and Vander Zanden 2010 ; Bootsma and Liao 2014 ; Mayer et al. 2014 ). The congener Dreissena rostriformis (the quagga mussel), while far less widespread than zebra mussels in inland waters, has ecologically replaced zebra mussels in much of the Laurentian Great Lakes proper and in deep European lakes, and may cause even greater ecological damage in those systems ( Karatayev et al. 2011b ; Matthews et al. 2014 ; Nalepa and Schloesser 2014 ).

Zebra mussel biogeography and genome sequencing strategy. (A) Photo of D. polymorpha (by Naomi Blinick). (B) Phylogenetic tree showing the evolutionary divergence between D. polymorpha and other sequenced bivalve genomes. For context, the evolutionary divergence of humans, mice, zebrafish, manta rays, nematodes, and fruit flies are shown. Grey text indicates that a genome sequence for that organism is not publicly available. Divergence times and tree construction based on Kumar et al. (2017) . (C–E) Maps depicting the spread of D. polymorpha in the United States of America from 1988 through 2018. Data from US Geological Survey, Non-indigenous Aquatic Species database ( USGS 2019a ). (F) Map showing the extent of zebra mussel infestation in Minnesota lakes as of 2018 and depicting the location where the specimens for genome sequencing and scaffolding were collected (left). Summary of the sequencing and annotation strategy (right).

The ongoing European and North American invasions ( Figure 1, C–E ) have spurred an explosion in research effort on Dreissena , particularly focused on physiology, autecology, and ecosystem impacts ( Schloesser and Schmuckal 2012 ). Aside from molecular systematic and population genetic studies ( Gelembiuk et al. 2006 ; May et al. 2006 ; Brown and Stepien 2010 ; Stepien et al. 2014 ; Mallez and McCartney 2018 ), comparatively little genetic work has been accomplished, with transcriptomes from a few tissues ( Xu and Faisal 2010 ; Soroka et al. 2018 ) being the only genomic resources available for zebra mussels.

Bivalves are a diverse Class of Mollusca with over 10,000 described species in marine and freshwater environments ( Bogan 2008 ; Appeltans et al. 2012 ). To date, complete genomes have been sequenced and analyzed in 30 species—many of them marine organisms of commercial value ( Figure 1B , Supplementary Table S1 ) ( Zhang et al. 2012 ; Gómez-Chiarri et al. 2015 ; Du et al. 2017 ; Li et al. 2017 ; Sun et al. 2017 ; Wang et al. 2017 ; Powell et al. 2018 ; Renaut et al. 2018 ; Uliano-Silva et al. 2018 ; Calcino et al. 2019 ; Ran et al. 2019 ; Yan et al. 2019 ; Gerdol et al. 2020 ; Kenny et al. 2020 ; Li et al. 2020 ; Liu et al. 2020 ; Wei et al. 2020 ; Bao et al. 2021 ; Gomes-Dos-Santos et al. 2021 ; Inoue et al. 2021 ; Ip et al. 2021 ; Rogers et al. 2021 ; Smith 2021 ; Song et al. 2021 ; Yang et al. 2021 ). Yet 21 invasive bivalve species cause damage to aquatic and marine ecosystems worldwide ( Sousa et al. 2009 ) and of these only the golden mussel, Limnoperna fortunei ( Uliano-Silva et al. 2018 ) and recently, the quagga mussel ( Calcino et al. 2019 ) D. rostriformis have so far been sequenced. Moreover, the divergence time between Dreissena and other bivalve species with published genomes is estimated at more than 400 million years ago ( Figure 1B ). Sequencing of the zebra mussel genome will provide a resource for comparative genomic and other studies of an underexplored lineage of bivalves that includes two of the world’s most notorious and damaging invasive species ( Lowe et al. 2000 ; Nalepa and Schloesser 2014 ).

Here, we present the genome sequence of D. polymorpha . Using short and long-read sequencing technologies as well as Hi-C-based scaffolding, we generated a chromosome-scale genome assembly with high contiguity and completeness. Through comparative analysis and RNA-sequencing (RNA-seq) experiments, we provide insights into the process of shell formation, the formation of byssal thread attachment fibers, and mechanisms of thermal tolerance—three processes of critical importance to continued spread. The genomic resources we describe lay the groundwork for further investigation of the traits that allow zebra mussels to thrive as an invasive species and are a step toward developing control strategies for this economically and ecologically damaging aquatic invader.

Genomic DNA extraction and PacBio library creation

Zebra mussel individuals were collected by SCUBA from off the Duluth waterfront beach (46.78671°N, –92.09114°W), in Lake Superior in June 2017. Mature adults were dissected. To sex the animals, gonad squashes were prepared and examined under a compound microscope for gametes, and a set of large males (25–30 mm shell length) were selected for genome sequencing and analysis. Genomic DNA was extracted using the Qiagen Genomic Tip 100/G kit, with all tissues (except gut) from each selected individual split across six total extractions to prevent clogging of Genomic Tips. Pooled extractions from one chosen individual yielded >100 ug genomic DNA as assessed by PicoGreen DNA quantification (ThermoFisher). The Agilent TapeStation Genomic DNA assay indicated that the majority of gDNA extracted was well over 20 kb (not shown). Further analysis by Pulsed-Field Gel Electrophoresis indicated a broad distribution from 20 to 120 kb, with a modal size of 40 kb (not shown).

Thirty micrograms of gDNA was sheared by passing a solution of 50 ng/uL DNA through a 26G blunt-tipped needle for a total of 20 passes. This sheared DNA was cleaned and concentrated using AMPurePB beads with a 1 × bead ratio, and further library preparation was performed following the PacBio protocol for >30kb libraries using the SMRTbell ® Template Prep Kit 1.0. Size-selection of the final library was carried out using the >20 kb high-pass protocol on the PippinHT (Sage Science), and an additional PacBio DNA Damage Repair treatment was performed following size-selection.

PacBio sequencing

Sequencing was carried-out on a PacBio Sequel between November 2017 and February 2018 using 1M v2 Single Molecule Real-Time (SMRT) Cells with 2.1 chemistry and diffusion loading.

Nanopore library creation and sequencing

Genomic DNA from the individual used for PacBio sequence was prepared for Nanopore sequencing using the Oxford Nanopore Ligation Sequencing Kit (SQK-LSK109). The resulting library was sequenced on a single Oxford Nanopore R9.4.1 flowcell on a GridION X5. Reads were collected in MinKNOW for GridION release 18.07.9 (minknow-core-gridion v. 1.15.4) and basecalled live with guppy v. 1.8.5-1.

Illumina polishing library creation and sequencing

High-molecular-weight DNA from the individual used for the PacBio sequencing was also used as input for Illumina TruSeq DNA PCR-Free library creation, targeting a 350 bp insert size. The resulting library was sequenced on a single lane of HiSeq 2500 High Output (SBS V4) in a 2 × 125 cycle configuration, yielding 68 gigabases (Gb) of data representing ∼37 × coverage of the genome.

Hi-C library creation and sequencing

A previously frozen male individual from the same collection date and site in Lake Superior was thawed and mantle, gonad, and gill tissues were dissected using a razor blade. This was a different mussel, because insufficient tissue remained after earlier DNA extractions of the other mussel for genome assembly and polishing. Hi-C library creation was carried out with a Proximo™ Hi-C kit (February 2018) from Phase Genomics using the Proximo™ Hi-C Animal Protocol version 1.0. This method is largely similar to previously published protocols ( Lieberman-Aiden et al. 2009 ). The resulting library was sequenced on a single lane of HiSeq 2500 High Output (SBS V4) in a 2 × 125 cycle configuration, yielding 234M clusters passing filter.

Sample collection for transcriptome studies

Adult zebra mussels (20–25 mm shell length) were collected from a high-Ca 2+ (35–38 mg/L) site: the Lake Ore-Be-Gone mine pit in Gilbert, MN (47.4836°N, –92.4605°W) and from a “low-Ca 2+ ” (14.4 mg/L) site: Lake Superior near the Duluth Lift Bridge (46.7867°N, 92.0911°W). Mussels and water were collected underwater by SCUBA, and mussels were stored on ice and returned to the laboratory for dissection within 6 h. This approach was used in lieu of experimental manipulations, because chronic exposure to low calcium concentrations are difficult to achieve in the laboratory—slow shell growth and poor survival have been observed in these marginal (< 15 mg/L) concentrations ( Baldwin et al. 2012 ). Calcium concentration in unfiltered, undigested lake water was determined by 15-element ICP-OES on the iCAP 7600 (Thermo-Fisher, Waltham, MA).

Gill and foot

For these transcriptomes, experiments were used to study differential gene expression in adult mussels that were housed in aquaria for several weeks where they were acclimated, fed laboratory diets, then exposed to experimental treatments. Zebra mussels (15–22 mm shell length) were collected from sites in Lake Minnetonka (44.9533° N, –93.4870° W and 44.8980° N, –93.6688° W) and Lake Waconia (44.8711° N, –93.7596° W) then transported in coolers to the University of Minnesota, where they were acclimated, 100 mussels per each of 12 × 40 L glass aquaria with flowing well water (4 L/min) at 20°C (unheated). Temperature was checked twice daily with digital probes. Mussels were fed 1.8 ml per tank of liquid shellfish diet (Reed Mariculture, Campbell, CA) once daily, with water flow shut off for 1.5 h for feeding. Tank temperatures were raised to 24–25°C over 3 days by mixing in heated well water; then temperatures were held constant over 7 days for acclimation.

Experimental treatments followed, with each group of four tanks raised 1°C per day (using a 200 W aquarium heater in each tank) to target temperatures of 25, 27, and 30°C then maintained at target for 7 days. For gill transcriptomes, two mussels per each of four treatment tanks were removed, then both ctenidia were dissected and preserved in 750 µL RNAlater per animal at –20°C. For foot, mussels from Lake Waconia, attached firmly to rocks and maintained for 7 days in each of two of the 25°C tanks above were selected. Byssal threads were severed where they enter the shell valves to induce byssus growth and reattachment. Immediately thereafter, foot tissue (distal tip region) was dissected from each of eight animals (for a time-zero control) and preserved in RNAlater. Byssus-cut animals were painted with nail polish and placed onto rocks in each of two tanks at 25°C. Mussels that firmly attached overnight were observed for 4 days and 8 days after reattachment, and four firmly attached mussels per time point were selected and foot tissue was dissected and preserved as above. Metadata for transcriptome samples is in Supplementary File S16 .

RNA-Seq sample preparation, library creation, and sequencing

Zebra mussel tissue RNA was extracted using the Qiagen RNeasy Plus Universal kit from tissues stored at –20°C in RNA later ™ (Ambion, Carlsbad, CA). RNA concentration was assessed using Nanodrop, and quantified fluorometrically with the RiboGreen RNA assay kit (ThermoFisher). Further evaluation was based on RNA Integrity Number (RIN) scores generated by the Agilent TapeStation 2200 Eukaryotic RNA assay. Samples with RIN >9.0 and RNA mass >500 ng were used as input for library preparation. Libraries were prepared using the TruSeq ® Stranded mRNA kit (Illumina) and sequenced on a HiSeq 2500 High Output (SBS V4) run in a 2 × 50 cycle configuration, generating approximately 15 M reads per sample (Mean = 15.8 M, 15% CV).

Genome assembly

The primary assembly was generated using Canu 1.7 ( Koren et al. 2017 ) from 167.8 Gbp of PacBio subreads over 1kbp in length with the command:

canu -p asm -d asm ‘genomeSize=2g’ ‘correctedErrorRate=0.105’ ‘corMinCoverage=4’ ‘corOutCoverage=100’ ‘batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50’ ‘corMhapSensitivity=normal’.

The assembly used heterozygous parameters due to the relatively high heterozygosity of the sample [2.13% estimated from Genoscope ( Vurture et al. 2017 ) and previous Illumina sequencing]. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis was run using BUSCO v3 ( Simao et al. 2015 ) and the metazoa_odb9 gene set with the command:

python run_BUSCO.py -c 16 –blast_single_core -f –in asm. contigs.fasta -o SAMPLE -l -m metazoa_odb9 genome.

The assembly had 93.9% core metazoan complete genes with 35.2% single copy complete and 58.7% duplicated complete genes. Purge haplotigs ( Roach et al. 2018 ) was run to remove redundancy in the assembly with the commands:

minimap2 -ax map-pb –secondary=no -t 16 asm.contigs.fasta reads.fasta.gz > reads.sam samtools view -b -T asm.contigs.fasta -S reads.sam > reads.bam samtools sort -O bam -o reads.sorted.bam -T tmp reads.bam samtools index reads.sorted.bam purge_haplotigs readhist reads.sorted.bam purge_haplotigs contigcov -i reads.sorted.bam.genecov -l 15 -m 80 -h 120 -j 200 purge_haplotigs purge -t 32 -g asm.contigs.fasta -c coverage_ stats.csv -b reads.sorted.bam -windowmasker

Unassigned contigs were removed from the primary set leaving 1.80 Gbp in 2863 contigs with an N50 of 1,111,027 bp.

Genome polishing

The resulting contigs were re-analyzed using the PacBio standard polishing pipeline—GenomicConsensus v2.3.3 ( Seifert and Alexander 2019 ), which derives a better genomic consensus through long read mapping and variant calling using an improved Hidden Markov Model implemented in the algorithm Arrow. The polished draft assembly was further corrected for Indels using Pilon ( Walker et al. 2014 ) with setting: –fix indels –threads 32 –verbose –changes –tracks. A single contig corresponding to the PacBio sequencing control was removed from the final assembly.

Repeat analysis

RepeatModeler ( Smit and Hubley 2008- 2015 ) was used to identify repeat families from the primary haploid genome. The resulted unknown repeat families were combined with the default full RepeatMasker ( Smit et al. 2019 ) database. RepeatMasker scanned the primary haploid genome sequences for the combined repeat databases in quick search mode.

Hi-C scaffolding

Chromatin conformation capture data were generated using a Phase Genomics (Seattle, WA) Proximo Hi-C Animal Kit v1.0, which is a commercially available version of the Hi-C protocol ( Lieberman-Aiden et al. 2009 ). Following the kit protocol, intact cells from two samples were crosslinked using a formaldehyde solution, digested using the Sau3A I restriction enzyme, and proximity-ligated with biotinylated nucleotides to create chimeric molecules composed of fragments from different regions of the genome that were physically proximal in vivo, but not necessarily proximal in the genome. Continuing with the manufacturer’s protocol, molecules were pulled down with streptavidin beads and processed into an Illumina-compatible sequencing library. Sequencing was performed in a single lane of Illumina HiSeq 2500 High Output (SBS V5) in a 2 × 125 cycle configuration, yielding 230,479,044 clusters passing filter.

Reads were aligned to the draft assembly also following the manufacturer’s recommendations ( Phase Genomics 2019 ). Briefly, reads were aligned using BWA-MEM ( Li and Durbin 2010 ) with the –5SP and –t 8 options specified, and all other options default. SAMBLASTER ( Faust and Hall 2014 ) was used to flag PCR duplicates, which were later excluded from analysis. Alignments were then filtered with samtools ( Li et al. 2009 ) using the –F 2304 filtering flag to remove non-primary and secondary alignments and further filtered with matlock ( Sullivan 2018 ) (default options) to remove alignment errors, low-quality alignments, and other alignment noise due to repetitiveness, heterozygosity, and other ambiguous assembled sequences.

Phase Genomics’ Proximo Hi-C genome-scaffolding platform was used to create chromosome-scale scaffolds from the corrected assembly as described ( Bickhart et al. 2017 ). As in the LACHESIS method ( Burton et al. 2013 ), this process computes a contact frequency matrix from the aligned Hi-C read pairs, normalized by the number of Sau3 AI restriction sites (GATC) on each contig, and constructs scaffolds in such a way as to optimize expected contact frequency and other statistical patterns in Hi-C data. Approximately 140,000 separate Proximo runs were performed to optimize the number of scaffolds to make them as concordant as possible with the observed Hi-C data. This process resulted in a set of 16 chromosome-scale scaffolds containing 1.76 Gbp of sequence (97.9% of the contig assembly), with a scaffold N50 of 117.5 Mbp and a scaffold N90 of 75.4 Mbp.

Mitochondrial genome assembly, polishing, mapping, and annotation

Mapping of PacBio reads to an initial Canu assembly for the mitochondrial genome indicated a small region of very high coverage ( Supplementary Figure S5 ). An alternate assembly of the mitochondrial genome was substituted which was generated in parallel in FALCON 0.5 (length_cutoff = –1, seed_coverage = 30, genome_size = 2.7G) and which did not collapse this repeat sequence. This assembly was polished for indels via Pilon using Illumina reads as with the nuclear genome, and a single substitution error in the coding region was manually edited (c.14475 C > A, G184W) based on strong support from Illumina reads (data not shown). The mitochondrial genome was annotated based a previously published partial mitochondrial sequence ( Soroka et al. 2018 ) in Geneious using the “Annotate from Database” function with a 98% similarity cutoff. The origin point was set to place the tRNA-Val annotation at base 48, matching the previously published sequence.

PacBio and Nanopore reads were mapped against a reference file containing two concatenated copies of the mitochondrial genome sequence to allow reads to map across the origin. Alignments were generated with minimap2 -ax using settings map-pb and map-ont, respectively. Visualization of the resulting alignments ( Figure 2C ) was performed using a custom tool, ConcatMap ( https://github.com/darylgohl/ConcatMap ). Illumina reads from the polishing library were mapped ( Supplementary Figure S5 ) to the final, polished mitochondrial genome using BWA-MEM ( Li and Durbin 2010 ).

D. polymorpha genome and mitogenome structure and content. (A) Plots depicting the gene content, repeat and transposon density, and GC content of the 16 D. polymorpha chromosomal scaffolds. (B) Proposed circular mitochondrial genome structure. GC content plots (blue) based on 40 bp sliding window. Annotations based on sequence similarity to previously published partial mitochondrial genome ( Soroka et al. 2018 ). Coding regions are in green and red, and the three large repeat blocks are colored turquoise, blue, and purple. (C) Plot of long (>25 kb) Oxford Nanopore (red) and PacBio (grey) reads supporting the proposed 67 kb circular mitogenome structure. Orientation of mitochondrial genome (blue) is the same as in (B).

Hi-C analysis of the mitochondrial contig

Ten contigs ranging in size from 50 kb to 100 kb were selected from each of the pseudo-chromosome scaffolds. The number of Hi-C contacts between each selected contig and each pseudo-chromosome was determined. The same analysis was performed using the mitochondrial contig, then all Hi-C link counts were normalized by dividing the number of contacts between a contig and pseudo-chromosome by the total number of Hi-C contacts associated with the contig. The resulting normalized data were visualized using ggplot2 to develop boxplots that compare the number of links for contigs based on their association with each pseudo-chromosome.

Transcriptome assembly

Reads from all zebra mussel RNA-seq libraries were pooled for transcriptome assembly. A database of ribosomal RNA was downloaded from SILVA ( Quast et al. 2013 ; Yilmaz et al. 2014 ; Glockner et al. 2017 ), restricting the entries to Bivalvia. The combined RNA-seq reads were cleaned of putative ribosomal RNA sequences using “BBDuk” from the BBTools suite of scripts ( Bushnell 2019 ), treating the Bivalvia ribosomal RNA as potential contaminants, using a k-mer size of 25 bp and an edit distance of 1. Reads that passed this filter were then assembled with Trinity 2.8.4 ( Grabherr et al. 2011 ) with a “RF” library type, in silico read normalization, and a minimum contig length of 500 bp. Assembled transcripts from Trinity were then searched against the non-redundant nucleotide sequence database hosted by NCBI, current as of October 9, 2018. A maximum of 20 target sequences were returned for each transcript, restricted by a minimum of 10% identity and a maximum E-value of 1 × 10 −5 . Assembled transcripts that matched sequences derived from non-eukaryotes or synthetic constructs were discarded.

Differential expression analysis

RNA-seq reads were checked for quality issues, adapter content, and duplication with FastQC 0.11.7. Cleaning for sequencing adapters, trimming of low-quality bases, and filtering for length were performed with Trimmomatic 3.3 ( Bolger et al. 2014 ). The adapter sequences that were targeted for removal were the standard Illumina sequencing adapters. Quality trimming was performed with a window size of 4 bp and a minimum mean quality score of 15. Reads that were shorter than 18 bp after trimming were discarded.

Reads were aligned to the HiC-scaffolded genome assembly draft with HISAT2 2.1.0 ( Kim et al. 2015 ), with putative intron–exon boundaries inferred with genes with functional annotation from the draft annotation and a bundled Python script. Read pairs in which one read failed quality control were not used in alignment and expression analysis. BAM files from HISAT2 were cleaned of reads with a mapping quality score of less than 60 with samtools 1.7. Cleaned alignments were used to generate expression counts with the featureCounts program in the Subread package v. 1.6.2 ( Liao et al. 2013 ). Both reads in a pair were required to map to a feature and be in the proper orientation for them to be counted. Raw read counts were imported into R 3.5.0 ( R Core Team 2018 ) for analysis with edgeR 3.24.3 ( Robinson et al. 2013 ). Genes that were less than 200 bp were removed from the counts matrix. Tests for differential expression were performed between experimental conditions within tissue. For each tissue, genes with low expression were filtered in the following way: genes in which at least X samples with fewer than 10 were removed, where X is the size of the condition with the fewest replicates. Tests for differential expression used a negative binomial model for dispersion estimation, and genes showing significant levels of differential expression were identified with a quasi-likelihood F test implemented in edgeR ( Lund et al. 2012 ). Genes were identified as differentially expressed if they had a nominal P -value of less than 0.01 in the output from the “glmQLFTest” function.

Tissue specificity calculation

Filtered, normalized counts were used to calculate τ, a measure of tissue specificity ( Yanai et al. 2005 ):

where N is the number of tissues analyzed and x i are the normalized counts. Normalized and log-transformed counts-per-million (CPM) values for each gene were estimated with edgeR. The mean CPM for samples from each tissue were treated as the expression values for that tissue. τ was then calculated for each gene. Genes with τ of 0.95 or greater were considered to be specific to the tissue with highest expression.

Identification of steamer-like elements and phylogenetic analysis

A sequence amplified from D. polymorpha using Steamer -like element (SLE)-targeting degenerate primers ( Metzger et al. 2018 ) was used as the basis for an initial BLAST search of the genome assembly. Dotplots of the sequence surrounding hits were analyzed to identify 50 putative Long Terminal Repeat (LTR) sequences, and these were aligned to build a consensus LTR sequence specific to our assembly. A subsequent BLAST search with this consensus sequence was performed, and surrounding sequence context was examined for the presence of long (>3 kb) open reading frames (ORFs) between flanking LTRs. Eight intact elements identified with these criteria were aligned based on coding sequence (ClustalW) and annotated based on NCBI Conserved Domain search.

First, we evaluated phylogenetic evidence that zebra mussel TEs are SLEs. Amino acid sequences for the full-length Gag-Pol polyprotein region from these eight elements and from the Steamer element from Mya arenaria (Accession AIE48224.1) were aligned to a database of the Gypsy/T3y family of LTR-retrotransposons ( Llorens et al. 2011 ), using MAFFT ( Katoh et al. 2017 ) and the E-INS-i method. The alignment included 2078 residues and 105 sequences. The model of sequence evolution was selected based on the AIC option in SMS ( Lefort et al. 2017 ), using the option to estimate amino acid frequencies from the data. A maximum likelihood genealogy was built using PhyML ( Guindon and Gascuel 2003 ), using the NNI tree topology search and the BIONJ starting tree options, and support for nodes was evaluated based on 100 bootstrap replications.

Next, we used DNA sequence genealogies to further investigate whether horizontal transmission of TE (HTT) events led to insertions of 20 SLEs that we found in the zebra mussel genome that contained two LTRs flanking an intact Gag-Pol ORF, including the eight elements above. From GenBank, we downloaded sequences from multiple bivalve species, from the region located between the RNase H and integrase domains of Gag-Pol that was amplified using degenerate primers ( Metzger et al. 2018 ). We added three sequences of long ORFs from Gag-Pol that were cloned from neoplastic tissue ( Metzger et al. 2016 ), three that were obtained from Crassostrea gigas and Mizuhopecten yessoensis genome projects, and the full length Steamer clone from M. arenaria. We used MAFFT and the G-INS-1 progressive method to align nucleotide sequences based on the translated amino acid sequences and trimmed the ends. The alignment of 54 sequences and 1074 nucleotide positions was loaded into PhylML and the maximum likelihood tree was constructed using the above options (except that in this case, nucleotide frequencies were optimized using maximum likelihood).

Genome annotation

Functional annotation was carried out with Funannotate 1.0.1 ( Palmer 2019 ) in haploid mode using transcript evidence from RNA-seq alignments, de novo Trinity assemblies, and genome-guided Trinity assemblies. First, repeats were identified using RepeatModeler ( Smit and Hubley 2008-2015 ) and soft-masked using RepeatMasker ( Smit and Hubley 2019 ). Second, protein evidence from a UniProtKB/Swiss-Prot-curated database (downloaded on April 26, 2017) was aligned to the genomes using tBLASTn and exonerate ( Slater and Birney 2005 ), and transcript evidence was aligned using GMAP ( Wu and Watanabe 2005 ). Analysis ab initio used gene predictors AUGUSTUS v3.2.3 ( Stanke and Morgenstern 2005 ) and GeneMark-ET v4.32 ( Besemer and Borodovsky 2005 ), trained using BRAKER1 ( Hoff et al. 2016 ), and tRNAs were predicted with tRNAscan-SE ( Lowe and Chan 2016 ). Consensus protein coding gene models were predicted using EvidenceModeler ( Haas et al. 2008 ), and finally gene models were discarded if they were more than 90% contained within a repeat masked region and/or identified from a BLASTp search of known transposons against the TransposonPSI ( Haas 2010 ) and Repbase ( Bao et al. 2015 ) repeat databases. Any fatal errors detected by tbl2asn ( https://www.ncbi.nlm.nih.gov/genbank/asndisc/ ) were fixed. Functional annotation used the following databases and tools: PFAM ( Finn et al. 2014 ), InterPro ( Jones et al. 2014 ), UniProtKB ( Apweiler et al. 2004 ), Merops ( Rawlings et al. 2016 ), CAZymes ( Lombard et al. 2014 ), and a set of transcription factors based on InterProScan domains ( Shelest 2017 ) to assign functional annotations.

Comparison to eastern oyster ( Crassostrea virginica ) proteins

Zebra mussel genes with functional annotation information were used to identify groups of genes orthologous to eastern oyster ( Crassostrea virginica ). Annotated protein sequences from C. virginica were downloaded from the C_virginica-3.0 assembly and annotation hosted on NCBI. Zebra mussel protein sequences and C. virginica protein sequences were grouped into orthologous groups using OrthoFinder version 2.2.7 ( Emms and Kelly 2018 ), OrthoFinder was run with BLASTP 2.7.1 for similarity searches, MAFFT 7.305 for alignment, MCL 14.137 for clustering, and RAxML 8.2.11 for tree inference.

To sequence the D. polymorpha genome, we used the strategy outlined in Figure 1F. We generated a size-selected PacBio library with ≥20 kb inserts ( Supplementary Figures S1 and S2 ). Using the PacBio Sequel SMRT sequencing platform, we generated 168.97 Gb of sequencing data for an estimated coverage over 100×, assuming a genome size (from densitometry measures of DNA content in stained nuclei) of 1.66 Gb ( Gregory 2003 ). The subread N50 for the PacBio reads was 16,524 bp, validating the high quality of the input DNA and PacBio sequencing library.

Canu ( Koren et al. 2017 ) yielded a 2.92 Gb assembly, with 15,311 contigs and a contig N50 of 549,263 bp. The assembly was 1.3 Gb larger than previously estimated ( Gregory 2003 ) due to the relatively high heterozygosity of the sample (2.13% estimated from GenomeScope and previous Illumina sequencing). Identification of allelic contigs ( Roach et al. 2018 ) removed redundancy and yielded a 1.8 Gb assembly containing 2863 contigs with a contig N50 value of 1,111,027 bp ( Table 1 ). Hi-C ( Bickhart et al. 2017 ) analysis of the polished assembly generated 16 scaffolds spanning 97.9% of the assembled genome (179 unscaffolded contigs comprised the remaining assembled material, Table 1 , Supplementary Figure S3 ). Earlier cytogenetic work found 1 N = 16 chromosomes for D. polymorpha ( Boroñ et al. 2004 ; Woznicki and Boroń 2012 ). The scaffold N50 value was >117 Mb and the scaffold L50 value was 6, consistent with a chromosome-scale assembly. The resulting scaffolds and contigs were checked for contamination from bacterial genomic DNA and sequencing adapters, and a single contig was removed because it mapped to the PacBio sequencing control.

Genome assembly statistics

Statistics summarizing the contiguity, completeness, and content of the D. polymorpha genome.

BUSCO analysis ( Simao et al. 2015 ) demonstrated that in addition to having high contiguity, the D. polymorpha genome assembly is highly complete, with >92% of eukaryotic and metazoan BUSCOs identified and <5% duplication ( Table 1 ). Also consistent with high completeness, 98.5% of the Illumina DNA sequencing reads mapped to the D. polymorpha assembly ( Table 1 , Supplementary Table S2 ).

Features of the D. polymorpha genome

The genome assembly was annotated using de novo as well as protein and transcript-guided methods. This analysis resulted in a list of 68,018 genes. Based on the number of genes typically present in other eukaryotic genomes, we believe this list is an overestimate of the number of bona fide zebra mussel genes. Ab initio gene prediction can introduce errors such as splitting genes based on allelic variation, fragmentation within the assembly, or failure to join exons ( Denton et al. 2014 ). The number of genes in the human genome was initially overestimated and this estimate has been refined over time using both experimental and computational methods ( Pertea and Salzberg 2010 ). Gene number estimates from other sequenced bivalves range from 24,045 ( Bai et al. 2019 ) to over 200,000 ( Renaut et al. 2018 ), with an average of around 41,000 estimated genes ( Smith 2021 ). Functional annotation was carried out by mapping to a number of databases, including PFAM ( Finn et al. 2014 ), InterPro ( Jones et al. 2014 ), UniProtKB ( Apweiler et al. 2004 ), Merops ( Rawlings et al. 2016 ), and CAZymes ( Lombard et al. 2014 ). Due to the large evolutionary divergence between D. polymorpha and other sequenced genomes, most of the predicted genes had no annotations assigned. However, 12,772 genes had recognizable orthologs.

Repetitive DNA is abundant in bivalve genomes ( Zhang et al. 2012 ; Li et al. 2017 ; Sun et al. 2017 ; Wang et al. 2017 ), which makes assembly challenging. The D. polymorpha genome is also highly repetitive (47.4% repetitive content, Figure 2A , Table 1 ) and AT-rich (35.1% GC). While a portion of this repetitive content could be assigned to long or short interspersed elements (LINEs or SINEs), or to known transposons. The majority of the repeats, or 34.4% of the genome, could not be classified ( Table 1 ).

The zebra mussel genome contains several notable gene family expansions ( Supplementary Figure S4, Files S1 and S2 ). D. polymorpha shows expansions of genes related to cellular stress responses and apoptosis that surpass humans and in several cases Pacific oyster ( C. gigas ; Zhang et al. 2012 ), including genes that encode the Hsp70s (heat shock chaperones), caspases (apoptosis), and Inhibitor of Apoptosis Proteins. Families of genes encoding the Cu-Zn superoxide dismutases (antioxidant defense) and C1q domain-containing proteins (innate immunity) show expansions that are, respectively, equal to and smaller than C. gigas , while cytochrome P450s (xeniobiotic detoxification) are contracted relative to humans ( Table 2 ). Given the large number of annotated genes in D. polymorpha , it should be noted that gene family sizes may have been overestimated.

Dreissena polmorpha gene family expansions

Selected gene family expansion data comparing D. polymorpha to Crassostrea gigas , Drosophila. melanogaster , and Homo. sapiens . Data for C. gigas , D. melanogaster , and H. sapiens from Zhang et al. (2012) .

Examination of orthology to eastern oyster ( C. virginica ) identified 10,065 orthologous groups ( Supplementary Files S3 and S4 ). A total of 26.3% of zebra mussel genes that were used for orthologous group identification were assigned to a group within C. virginica . This is consistent with the low sequence similarity between zebra mussel and C. virginica , even at the amino acid level. A majority (5753; 57.16%) of the orthologous groups involved equal numbers of genes from zebra mussel and C. virginica . Of orthologous groups of unequal size, there were far more groups with contracted than expanded gene families in zebra mussel, relative to this distantly related bivalve (76.86% contracted and 23.14% expanded).

In the initial assembly, we recovered a single contig containing the D. polymorpha mitochondrial genome ( Figure 2B ). A partial D. polymorpha mitogenome sequence was previously published ( Appeltans et al. 2012 ), but contained a gap which short-read sequencing and targeted PCR were unable to resolve. PacBio and Oxford Nanopore sequencing ( Figure 2C ) reveals that this “gap” is a large highly repetitive segment of nearly 50 kb, making the D. polymorpha mitogenome the largest reported so far from Eumetazoa at 67,195 bp. The repetitive segment consists of three distinct blocks of direct tandem repeats ( Supplementary Figure S5 ), with individual repeat elements of approximately 125 bp, 1030 bp, and 86 bp, each copied many times. The 86 bp repeat element was discovered only after re-mapping of long reads to the initial assembly, which indicated an area of especially high coverage and read-clipping ( Supplementary Figure S6 ). An alternate mitochondrial assembly generated using FALCON revealed this anomaly to be an additional repeat sequence, to which the PacBio and Oxford Nanopore reads mapped seamlessly. Thus, the FALCON mitogenome assembly has been used in datasets associated with this paper ( Figure 2, B and C ). We further validated that the mitochondrial contig was not associated with chromosomal sequences by examining Hi-C data, where the association between the mitochondrial contig and the D. polymorpha chromosomes was much lower than the association between contigs on the same scaffold and was comparable to background levels of crosslinking seen between contigs on different scaffolds ( Supplementary Figure S5 ). Eumetazoan mitogenomes, with few exceptions, generally lack length variation and non-coding DNA content ( Soroka et al. 2018 ). Among these few exceptions are the long enigmatic mitogenomes of scallops ( Boore 1999 ), but unlike scallops, the coding genes of D. polymorpha remain contiguous, instead of being interrupted by interspersed repeats. Typical of animals, the coding region in D. polymorpha is compact (∼17.5 kb), but the order of mitochondrial genes is unique to the species, a finding that is common in bivalves ( Boore 1999 ). The reason for this unusual mitochondrial DNA (mtDNA) structure is unknown, but similar repetitive sequences have been observed in the mtDNA of plants where it has been suggested that such repeats may result from increased double-stranded break repair in response to desiccation-related DNA damage ( Wynn and Christensen 2019 ).

Some mussels exhibit doubly uniparental inheritance (DUI) of mtDNA, or transmission of two gender-associated mitogenomes: an F-type through eggs and M-type through sperm ( Breton et al. 2007 ; Doucet-Beaupré et al. 2010 ). DUI is present in Venerupis ; i.e . in Superorder Imparidentia, containing Dreissenidae. We found no evidence for a second divergent mitogenome. We located no other contigs (via tblastx) that contain mitochondrial genes. Furthermore, re-mapping of high-accuracy Illumina reads from the same mussel to the mitochondrial genome revealed no SNPs within the coding region ( Supplementary Figure S6 ), indicative of homoplasmy. The tissues used for DNA extraction included ripe male gonad with abundant motile sperm. With DUI, extracts would be expected to contain both mtDNAs, as the M-type is transmitted exclusively through male germline, while in somatic tissues, the F-type is predominant ( Breton et al. 2007 , 2010 ).

Steamer -like elements

We identified a number of LTR retrotransposons that are similar in structure to Steamer , a transposable element (TE) that in the soft-shelled clam M. arenaria causes a leukemia that is transmissible between conspecifics ( Arriagada et al. 2014 ; Metzger et al. 2015 ). A high incidence of HTT has spread these SLEs across several bivalves that also contract transmissible cancers, and across phyla to several marine animal species that do not ( Metzger et al. 2018 ). We identified eight copies of putative SLEs in the D. polymorpha genome with intact polycistronic ORFs that span the conserved Gag-Pol polyprotein and are flanked by LTRs ( Figure 3A ). The D. polymorpha elements were aligned to the full length ORFs of 99 Ty3/Gypsy LTR-retrotransposons. Phylogenetic analysis confirmed that the TEs in D. polymorpha are SLEs ( Supplementary Figure S7 ). The D. polymorpha elements grouped within the Mag C clade with 100% bootstrap support, and sister to Steamer. Next, we performed phylogenetic analysis of the D. polymorpha elements and amplicons from within the RNaseH-integrase domain of Gag-Pol from 47 other bivalve species, characterized in an earlier study of HTT events ( Metzger et al. 2018 ). Our phylogenetic analysis identified a minimum of three HTTs leading to their spread to zebra mussels from marine bivalves ( Figure 3B ), including an independent event in additional to the two HTTs identified previously ( Metzger et al. 2018 ). It is unknown whether SLEs are currently undergoing active transposition within zebra mussels. However, the high levels of sequence similarity between Gag-pol regions of different SLE loci, and between the two LTRs of each SLE, indicates that the latest wave of transposition in this genome was recent. We also identified numerous degenerate copies that are missing portions of Gag-Pol or LTR sequences, as well as isolated LTR scars on most chromosomes ( Supplementary Figure S8 ).

SLEs in the D. polymorpha genome. (A) Schematics depicting the eight SLE copies, each with two LTRs flanking the longest ORFs among all similar elements in the D. polymorpha genome. (B) Maximum likelihood phylogenetic tree of nucleotide sequences from the RNaseH-integrase domain of Gag-Pol in D. polymorpha and other bivalve SLEs. The selected model ( Anisimova et al. 2011 ) of DNA sequence evolution was the GTR + G (rates Γ-distributed, α = 1.190) + I (estimated proportion of invariant sites = 0.011). The tree was rooted on the Polititapes aureus 2/3/ Mercenaria mercenaria branch (bottom) and bootstrap support values > 70 are shown. Colored boxes A, B, and C contain taxa involved in all HTT events within bivalves that were identified previously ( Metzger et al. 2018 ). Arrows label HTT events 1 and 2, identified previously ( Metzger et al. 2018 ) and HTT 3, which we identified based on the same criteria. Together these account for two independent insertions of SLEs into zebra mussels. Clade D contains SLE sequences from the zebra mussel genome; “ D. polymorpha C” = chromosomal location of the SLE, with letters to order multiple insertion sites. Taxon labels include NCBI Accession number, taxon , followed by isolate number or code. ∗ = Sequence is from full length ORF encoding Gag-Pol , † = pseudogene sequence (one or more stop codons), § = sequence derived from neoplastic hemocytes ( Metzger et al. 2016 ).

Tissue-specific gene expression

We next conducted several RNA-Seq experiments to identify genes that are expressed in a tissue-specific manner, or genes that are regulated in response to different experimental conditions. We examined gene expression in the following tissues ( Figure 4A ): mantle (the organ that secretes shell), gill (the focal organ for thermal stress response), and foot (the organ that forms and attaches the byssal threads). RNA-Seq data from these three tissues was mapped to the reference containing the 68,018 annotated genes. A tissue-specificity index (τ) ( Yanai et al. 2005 ) was calculated and 577 genes exceeded the threshold of τ = 0.95 ( Figure 4B , Supplementary Figure S9 and Files S5–S7 ). Mantle contained the most tissue-specific genes—359 or 62.2% of the total unique transcripts. Tissue-specific genes had relatively little overlap with genes that were differentially expressed under the experimental conditions tested, suggesting that most tissue-specific genes are carrying out core as opposed to regulated functions ( Supplementary Figure S9 and Files S8–S10 ).

Tissue-specific gene expression patterns: mantle gene expression analysis. (A) D. polymorpha : lateral view of the left valve with the right valve and the covering mantle fold removed to reveal the organs dissected for transcriptomes. In purple is the margin of the mantle tissue within the left valve. In D. polymorpha , the mantle tissue is fused to form the siphons. Inhalent and exhalant siphon openings are pictured, as is the gill (ctenidium). Modified from Yonge and Campbell (2012) . (B) Heatmap depicting Z-scores for tissue-specific gene expression in the foot, gill, and mantle. (C) List of the most highly expressed mantle-specific genes (tau > 0.95). (D) Gene ontology term enrichment analysis for the mantle-specific genes.

Mantle gene expression and shell formation

In dreissenids and other bivalves, the shell is constructed of calcium carbonate of different crystal forms (typically calcite in adult and aragonite in larval shells) that are deposited in an organic matrix, either through an extracellular or cell-mediated mechanism ( Weiner and Traub 1984 ; Mount et al. 2004 ). Positive correlations between ambient Ca 2+ and shell strength and calcification have been found in some freshwater mollusk species, and selection favoring shell strength to aid in predator defense has been detected in others ( Russell-Hunter et al. 1981 ; Lewis and Magnuson 1999 ). To identify biomineralization-related genes, we dissected mantle from adult zebra mussels. We collected mussels from both a calcium-rich (Lake Ore-be-gone: 35.4 mg/L) and a calcium-poor (Lake Superior: 14.4 mg/L) water body.

By inspecting highly expressed mantle-specific genes using the automated annotations as well as BLASTp and comparison with published gene lists ( Zhang et al. 2012 ), we identified orthologs of a set of genes that have been previously implicated in shell formation ( Figure 4C , Supplementary File S11 ). These include tyrosinases, which are required for DOPA production, and other proteins that likely have structural roles, such as collagen. Transcripts for six shematrin-like proteins were among the most specific and highly expressed in mantle. Shematrins are glycine-rich shell matrix proteins that are expressed in the mantle of other mollusks ( Yano et al. 2006 ; Jackson et al. 2010 ; McDougall et al. 2013 ; Lin et al. 2014 ). Glycine-rich peptides in other organisms include structural proteins in rigid plant cell walls (60–70% glycine residues) as well as the major connective tissue in animals, collagen ( Shoulders and Raines 2009 ; Ringli et al. 2001 ). The exact function of shematrins in shell formation is not clear, but their high expression levels and unusual structure is intriguing; D. polymorpha shematrins are characterized by arrays of G(n)Y repeats ( Supplementary Figure S10 ). The zebra mussel shematrin proteins cannot be aligned to shematrins of pearl oyster Pinctada fucata , from which they were first characterized. However, the proteins in both genera share features. All are basic, with long runs of compositional bias including glycine-rich tandem repeats ( Supplementary Figures S11 and S12 , File S12 ). Functional studies of bivalve shematrin-like proteins are greatly needed.

Also highly expressed in the mantle were transcripts that encode a number of Sushi, von Willebrand factor Type A, EGF, and pentraxin domain-containing proteinsthat have been implicated in osteogenesis in mammals and have been identified in the mantle of other bivalves. In contrast to shell formation in pearl oysters ( Takeuchi et al. 2016 ), no nacrein genes were identified in the zebra mussel genome and a tBLASTn search of the zebra mussel genome with P. fucata nacrein yielded no hits. Gene ontology term enrichment analysis also showed that the chitin-binding molecular function was significantly enriched in the mantle-specific genes, along with a number of peptidase inhibitors ( Figure 4D ).

Among the most specific and highly expressed mantle genes in D. polymorpha were two genes with sequence similarity to temptin , which encodes a pheromone that serves as a chemoattractant for mating in the sea hare Aplysia ( Cummins et al. 2004 ). Zebra mussels attach to one another in clusters known as druses. Settlement of larvae near adults ( Wainman et al. 1996 ) and gregarious post-settlement behaviors ( Tošenovský and Kobak 2015 ) create massive aggregations on lake and river bottom. These behaviors increase settlement success, enable “habitat engineering” in mussel beds ( Tošenovský and Kobak 2015 ), and may enhance feeding and fertilization success ( Quinn and Ackerman 2011 , 2012 ; Nishizaki and Ackerman 2017 ). BLAST searches of the genomes of D. polymorpha , other bivalves, and Aplysia ( Supplementary Figures S13 and S14 ) found several additional proteins that share the temptin calcium-binding epidermal growth factor-like domain. Further studies are needed to determine if D. polymorpha temptin-like proteins serve chemosensory roles, for instance in synchronizing spawning, in sperm attraction, in settlement of larvae near adults ( Wainman et al. 1996 ), or in gregarious post-settlement behaviors ( Tošenovský and Kobak 2015 ).

Insights into byssal thread formation and attachment

The fibers that zebra and quagga mussels use to anchor themselves to hard surfaces are known as byssal threads. These are key innovations (absent from native North American and European freshwater mollusks) used to attach to conspecific mussels, and to native unionid mussels and other benthic animals that can be smothered and outcompeted. Byssal attachment to boat hulls, docks, boat lifts, and other recreational equipment allows rapid rates of spread between water bodies ( Johnson et al. 2001 ; De Ventura et al. 2016 ; Collas et al. 2018 ). Expression of genes during byssogenesis has been studied in zebra mussels ( Xu and Faisal 2010 ) but a majority of mRNAs that are up or down-regulated could not be identified.

Previous work identified a full byssal protein cDNA sequence (named Dpfp1) ( Anderson and Waite 1998 , 2000 ) and peptide fragments from a second byssal protein in the foot, the structure that secretes and anchors the threads ( Rzepecki and Waite 1993 ). More recent proteomic work also identified peptide tags associated with several D. polymorpha foot proteins that are secreted by the foot and together form the stem, threads, and attachment plaques ( Figure 5 ) of the byssus ( Gantayet et al. 2013 ). Sequences and chromosomal locations of all the genes encoding these byssal proteins are resolved in the zebra mussel genome ( Supplementary File 13 ). The byssalome includes 37 loci on 10 of the 16 zebra mussel chromosomes ( Figure 5B ). Duplications have generated multiple copies of the byssal genes; some in clusters on single chromosomes, others dispersed onto different chromosomes on both strands ( Figure 5B ). Duplications are especially abundant in the Dpfp7 and Dpfp9 families, generating substantial amino acid coding variation between the paralogs (not shown). A recent publication provides further detail on the characterization of the zebra mussel byssal thread genes ( McCartney 2021 ).

Byssal genes. (A) SEM image of byssus, consisting of threads and plaques. (B) Chromosomal location of the 37 loci predicted to encode 38 byssal protein variants. Chromosomal contigs (blue shaded ovals) are numbered (italics) in order of decreasing size. Byssal genes labeled above the chromosomes are on (+) strands; below are on (−) strands. Byssal protein Dpfp7 has three (α, β, γ) and Dpfp 11 has two (α, β) classes of divergent variants. Chromosome lengths and gene coordinates are in megabases (Mb). To the right of panel B are chromosomes 8 and 9, on which byssal genes are abundant. Modified from McCartney (2021) .

We also examined transcripts from the foot following experimental induction of byssogenesis ( Xu and Faisal 2010 ) ( Supplementary Figure S15 ). The foot distal to the byssus was dissected immediately after severing the byssal threads, and 4 and 8 days later. Changes were observed at the day-4 time point, after which expression broadly returned to baseline by day 8 ( Supplementary Figure S15 ). Some of the up-regulated genes were consistent with function identified in previous work on byssogenesis in the scallop ( Li et al. 2017 ), including tenascin-X (a connective protein) and a gene with phospholipid scramblase activity (Anoctamin-4-like, Supplementary Figure S15 and File S14 ). In addition, there was a clear inhibition of the tumor necrosis factor (TNF) pathway, with down-regulation of a TNF-ligand-like protein and up-regulation of Tax1BP1 (a negative regulator of TNF-signaling). The TNF pathway regulates inflammation and apoptosis, suggesting that production of the byssal thread may induce stress in the surrounding tissues and that this stress response may be actively suppressed. Consistent with this, both a cytokine receptor and the pro-apoptotic Bcl2-like gene are down-regulated at the day-4 time point. While earlier expression studies found otherwise ( Xu and Faisal 2010 ; Gantayet et al. 2013 , 2014 ), some byssal proteins were absent from our differentially expressed gene set. And while some of these proteins are differentially distributed across the byssus, localized expression in the foot has not been studied. Nevertheless, one explanation is that our dissections missed the secretory cells more proximal to the threads, a possibility that awaits testing.

Thermal tolerance and chronic heat stress

In Dreissena , broad thermal tolerance and ability to adjust to local conditions have clearly played a role in invasion success. Zebra mussels have higher lethal temperature limits and spawn at higher water temperatures in North America than in Europe ( McMahon 1996 ; Nichols 1996 ). In the Lower Mississippi River, zebra mussels are found south to Louisiana. There they lack cooler water refuges, and persist near their lethal limit of 29–30°C for 3 months during the summer, while for 3 months, temperatures in the river range from 5 to 10°C ( Allen et al. 1999 ). In contrast, zebra mussels in the Upper Mississippi River encounter water temperatures > 25°C for just 1 month of the year, and <2°C for about 3 months ( USGS 2019b ). Seasonal scheduling of growth and reproductive effort appears to be responsible for at least some of the adaptation or acclimation to conditions in the lower river, as populations in Louisiana shift their shell and tissue growth to the early spring and stop growing in summer ( Allen et al. 1999 ) while more northerly populations grow tissue and spawn in summer months ( Borcherding 1991 ; Claxton and Mackie 1998 ).

To identify genes involved in the response to thermal stress, we generated transcriptomes from gill tissue in animals exposed to periods of low (24°C), moderate (27°C), and high (30°C) chronic temperature stress ( Figure 6A ). Moderate thermal stress led to the induction of several genes involved in cellular adhesion or cytoskeletal remodeling, including collagen, gelsolin, MYLIP E3 ubiquitin ligase, and N-cadherin ( Figure 6B , Supplementary File S15 ). High thermal stress led to strong induction of a large number of chaperones, including HSP70, DNAJ, Calnexin, and HSC70 (several of which were also induced to a lesser extent under moderate thermal stress), as well as the antioxidant protein cytochrome P450 ( Figure 6, B and C , Supplementary File S15 ). The list of down-regulated genes was quite similar for both the moderate and high thermal stress conditions ( Figure 6, D–E , Supplementary File S15 ). In addition to the induction of known stress-response genes, a number of genes with unknown function are also regulated by thermal stress, as is 4-Hydroxyphenylpyruvate Dioxygenase, an enzyme which is involved in the catabolism of tyrosine ( Figure 6, B–E , Supplementary File S15 ).

Response of D. polymorpha to thermal stress. (A) Overview of experimental set-up. Animals were subjected to low (24°C), moderate (27°C), and high (30°C) thermal stress ( n = 4 animals per condition). (B) Top 20 genes upregulated during moderate thermal stress by log2 fold-change. (C) Top 20 genes upregulated during high thermal stress by log2 fold-change. (D) Top 20 genes downregulated during moderate thermal stress by log2 fold-change. (E) Top 20 genes downregulated during high thermal stress by log2 fold-change. Genes highlighted in red encode chaperone proteins.

Here, we describe the genome of the zebra mussel. Consistent with the genomes of other bivalves, the D. polymorpha genome is highly repetitive and encodes an expanded set of heat-shock and anti-apoptotic proteins, presumably to deal with the challenges of a sessile existence. We examine the genetic underpinnings of several traits that have been linked to population growth and invasiveness, including shell and byssal thread formation, and response to thermal stress. While these analyses uncovered multiple genes and pathways that seem to function in a conserved manner across multiple bivalve species, they also uncovered many genes of unknown function. In the future, it will be of considerable value to compare the zebra mussel genome with that of its congener, the quagga mussel ( D. rostriformis ), in order to gain further insights into ecological displacement of zebra mussels by quagga mussels, and to investigate genetic underpinning of their relative invasiveness, such as comparative work on byssogenesis that may help account for the slower geographic spread of quagga mussels ( Karatayev et al. 2011a ).

The existence of genomic resources for D. polymorpha and the catalog of genes we have identified will enable multiple new lines of investigation, as well as provide researchers with an improved tool for population genetic experiments, for instance, tracking the spread of mussels using Genotyping-by-Sequencing approaches, or designing new targeted assays for the presence or activity of zebra mussels.

While it is clear that changes in transportation networks ( e.g. canal building, opening of shipping channels, ballast water discharge) were the events that initiated primary invasions of European and North American waters ( Karatayev et al. 2007 ; Pagnucco et al. 2015 ), several biological characteristics are responsible for the rate of spread of zebra and quagga mussels across both continents, while other traits have limited their suitable habitat range. Genomics offers a path to understanding these traits at the genetic level, which may ultimately guide the development of control methods and management strategies.

Data availability

Supplementary material, jkab423_supplementary_figures, jkab423_supplementary_files, jkab423_supplementary_figure_legends_and_file_descriptions, acknowledgments.

This work utilized the computational resources of the NIH HPC Biowulf cluster ( https://hpc.nih.gov ) and the Minnesota Supercomputing Institute ( https://www.msi.umn.edu ).

Author Contributions

M.A.M. and D.M.G. conceived and designed experiments, analyzed data, and wrote the paper. B.A. prepared PacBio and Hi-C libraries, analyzed data, and wrote the paper. T.K., Y.Z., J.E.A., and K.A.T.S. analyzed data and helped to assemble and annotate the genome. S.M. designed experiments, collected samples, isolated DNA. J.G. analyzed data. A.O. and E.D.S. analyzed byssal thread attachment proteins. A.B. carried out sequencing of PacBio and Illumina libraries. J.P.B. carried out nanopore sequencing. A.H. and H.M. analyzed data. I.L., H.M., and S.S. carried out Hi-C-based scaffolding. S.K. generated the Canu assembly and ran purge haplotigs. K.B.B. conceived and designed experiments.

S.K. is supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health. Funding was from the Minnesota Environment and Natural Resources Trust Fund and the Minnesota Aquatic Invasive Species Research Center.

Conflicts of interest

I.L. and S.S. have a financial interest in and are directors of Phase Genomics, a company commercializing proximity ligation technology. H.M. is an employee of Phase Genomics.

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Zebra versus quagga mussels: a review of their spread, population dynamics, and ecosystem impacts

• INVASIVE SPECIES
• Review Paper
• Published: 16 May 2014
• Volume 746 , pages 97–112, ( 2015 )

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• Alexander Y. Karatayev 1 ,
• Lyubov E. Burlakova 1 , 2 &
• Dianna K. Padilla 3  

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Dreissena polymorpha (zebra mussel) and D. rostriformis bugensis (quagga mussel) continue to spread in Europe and in North America, and have large ecological and economic impacts where they invade. Today many more waterbodies are invaded by zebra mussels, and therefore the extent of their impact is greater than that of quagga mussels. Both species provide additional space and food for invertebrates in the littoral zone, increasing their diversity and density. In contrast, in the profundal zone, quagga mussels may compete for space and food resources with benthic invertebrates, decreasing their diversity and density. The system-wide effect of dreissenids depends on water mixing rates, lake morphology, and turnover rates. Because quagga mussels are found in all regions of a lake, and form larger populations, they may filter larger volumes of water and may have greater system-wide effects, especially in deep lakes, than zebra mussels, which are restricted to shallower portions of lakes. Shortly after initial invasion, as populations increase, both dreissenids will have their largest effects on communities, and most of them will be direct effects. After the initial stage of invasion, impacts are less predictable, and more likely to be caused by indirect effects through changes in the ecosystem.

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Karatayev, A.Y., Burlakova, L.E. & Padilla, D.K. Zebra versus quagga mussels: a review of their spread, population dynamics, and ecosystem impacts. Hydrobiologia 746 , 97–112 (2015). https://doi.org/10.1007/s10750-014-1901-x

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Received : 20 January 2014

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Accepted : 26 April 2014

Published : 16 May 2014

Issue Date : March 2015

DOI : https://doi.org/10.1007/s10750-014-1901-x

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Here's what's missing from the invasive species narrative

Hannah Chinn

Emily Kwong

Rebecca Ramirez

Shells, composed mostly of invasive zebra mussels pile up at Sleeping Bear Dunes National Lakeshore in Michigan. The Nonindigenous Aquatic Nuisance Species Control and Prevention Act of 1990 and the United States Geological Survey's Nonindigenous Aquatic Species database were created in response to this mussel. corfoto/Getty Images hide caption

Shells, composed mostly of invasive zebra mussels pile up at Sleeping Bear Dunes National Lakeshore in Michigan. The Nonindigenous Aquatic Nuisance Species Control and Prevention Act of 1990 and the United States Geological Survey's Nonindigenous Aquatic Species database were created in response to this mussel.

At first glance, the whole narrative of aquatic invasive species may seem straightforward. A non-native, invasive species comes in and dukes it out against native species to become the top dog. The losing native species are good guys; the non-native species are bad guys.

We see this narrative time and again with coverage of species — like the spotted lanternfly and the Joro spider.

Fighting An Insect Invasion With... An Insect Invasion

Why you shouldn't worry about invasive Joro spiders

But what makes a species as invasive? How can we prevent them from taking over? And what's the best way to deal with them once they're already here?

Over the years, management strategies have run the gamut — from spraying pesticides to releasing competitive organisms and running an annual python-hunting challenge .

Part of the problem in combating invasive species is that "by the time we're seeing these species, they're already established, they're already taking over," says Ian Pfingsten , a botanist who works on the United States Geological Survey's Nonindigenous Aquatic Species Database . That means researchers like Pfingsten are frequently trailing these species rather than getting ahead of them.

All of that education and documentation is key to researchers understanding the scope of a species' spread. But it still only tells part of the invasive species narrative.

"I see a lot of scapegoating in the form of — if we can get rid of that species, then we've solved the problem," says Nicholas Reo , a Canada Excellence Research Chair in Coastal Relationalities and Regeneration. "But I kind of see that as as a bit of a Band-Aid approach."

When tiny, invasive ants go marching in ... and alter an ecosystem

That's because the main cause of invasive species spread is human activity.

"Shipping, transports, commerce, trade ... it's typically through some kind of economic means," Pfingsten says.

To get at the root of the problem, Reo says we humans have to take a concerted look in the mirror — even if it means being slower and stricter about the flow of commerce. Reo also pushes for experts to establish relationships with indigenous peoples who have longstanding relationships with the species — and, in turn, often know how to keep them in check.

Have a favorite invasive species or one that you really can't stand? Email us at [email protected] — we'd love to hear your take!

Listen to every episode of Short Wave sponsor-free and support our work at NPR by signing up for Short Wave+ at plus.npr.org/shortwave .

Listen to Short Wave on Spotify and Apple Podcasts .

This episode was produced by Hannah Chinn. It was edited by Rebecca Ramirez. They both checked the facts. Kwesi Lee was the audio engineer.

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Zebra mussels found in Big Carnelian Lake, Minnesota DNR says

Invasive zebra mussels have been confirmed in Big Carnelian Lake in northern Washington County.

Officials with the Minnesota Department of Natural Resources recently received a report of a zebra mussel attached to riprap on the lake’s shoreline. A crew from the DNR, along with staff from the Washington Conservation District and Carnelian-Marine-St. Croix Watershed District, conducted a search of the lake and found adult zebra mussels at the all sites they searched. They also found zebra mussel larvae, called veligers, in water samples that were taken at the lake.

State law requires boaters, anglers and waterfront property owners to take a variety of actions to prevent the spread of zebra mussels, regardless of whether a lake has an infestation, according to the DNR.

People should contact a Minnesota DNR aquatic invasive species specialist if they believe they have found zebra mussels or any other invasive species not already known to be in the water body.

Zebra mussels can compete with native species for food and habitat, cut the feet of swimmers, reduce the performance of boat motors and damage water-intake pipes.

More information is available at mndnr.gov/zebramussels .

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Fisheries and Oceans Canada conducts second roadside inspection blitz to prevent the spread of Zebra Mussels

From: Fisheries and Oceans Canada

News release

Zebra Mussels are an aquatic invasive species that reproduce very quickly, cause negative ecological impacts, deteriorate infrastructure, and negatively impact the economy. Since being introduced into the Laurentian Great Lakes region in the 1980s, Zebra Mussels have spread to southern Ontario, south and central Manitoba, southern Québec and New Brunswick, and are a growing threat.

August 30, 2024

Winnipeg, Manitoba - Zebra Mussels are an aquatic invasive species that reproduce very quickly, cause negative ecological impacts, deteriorate infrastructure, and negatively impact the economy. Since being introduced into the Laurentian Great Lakes region in the 1980s, Zebra Mussels have spread to southern Ontario, south and central Manitoba, southern Québec and New Brunswick, and are a growing threat.

Fisheries and Oceans Canada (DFO) is taking action to prevent the introduction and spread of all AIS, including Zebra Mussels. This summer, DFO conducted roadside inspections along the Trans-Canada Highway at the Manitoba and Ontario border. Following the success of the first blitz weekend in June, DFO’s Aquatic Invasive Species Program staff and fishery officers, provincial AIS inspection staff and conservation officers from the Manitoba Department of Economic Development, Investment, Trade and Natural Resources, conducted another blitz from August 23 to 25 with equally impressive results. This time, a total of 451 vehicles were stopped that were transporting watercraft and travelling across the provincial boundary.

Prevention is the most efficient, practical and cost-effective approach to managing AIS, including Zebra Mussels. Cleaning, draining and drying all watercraft and water-related equipment when either removing them from the water and/or before placing them into another waterbody is key to preventing the spread of AIS. Of the 451 vehicles that were stopped between August 23 and 25:

• 153 vehicles were transporting watercraft or equipment that were not clean, drained, or dry and failed the AIS inspection.
• 225 vehicles transporting watercraft were compliant with clean, drain, dry requirements.
• 0 watercraft had Zebra Mussels visible.

Drivers transporting non-compliant watercraft had their watercraft and equipment decontaminated, and were given instructions for how to comply with the clean, drain, dry requirements.

“Aquatic invasive species threaten Canada’s biodiversity, economy, and infrastructure. By working together with provinces, territories and other partners on enforcement and educational activities, we can prevent the further spread of species like Zebra Mussels, protecting Canada’s waterways and ensuring a healthier environment for all Canadians.” The Honourable Diane Lebouthillier, Minister of Fisheries, Oceans and the Canadian Coast Guard

“Our government remains committed to battling AIS and taking action through education and enforcement to halt the spread. Manitoba was proud to release the Aquatic Invasive Species (AIS) Prevention and Response Plan this summer to set out a way forward for AIS prevention. The plan emphasizes the need to work collaboratively towards a responsive, nimble inspections program. The inspections that took place this weekend are an excellent opportunity to educate the public and stop zebra mussels from being transported.” The Honourable Jamie Moses, Minister of Economic Development, Investment, Trade and Natural Resources

Quick facts

Aquatic invasive species are freshwater or marine plants, animals, algae and micro-organisms introduced outside their natural or past distribution. They have significant negative impacts on the environment, economy, society and human health.

During DFO’s June inspection blitz along the Trans-Canada Highway between Manitoba and Ontario:

• 294 vehicles transporting watercraft were compliant with clean, drain, dry requirements.
• 104 vehicles were transporting watercraft or equipment that were not clean, drained, or dry and failed the AIS inspection.
• Five vehicles were found to be transporting Zebra Mussels.

AIS pose a serious threat to the biodiversity of Canada’s waters. After habitat loss, invasive species are the second biggest threat to global biodiversity. They can grow quickly, compete with native species and alter habitats, and cost billions of dollars annually in damages to infrastructure and revenue loss in Canada.

Under the Aquatic Invasive Species Regulations it is illegal to possess, transport, and release Zebra Mussels in Manitoba, Saskatchewan, Alberta and British Columbia. It is also illegal to import Zebra Mussels into Canada, except within the transboundary waters of the Great Lakes in Ontario and transboundary waters of Quebec.

Associated links

• Clean, Drain, Dry and Decontaminate
• Aquatic Invasive Species Regulations
• Identify an aquatic invasive species
• Report an aquatic invasive species

Gabriel Bourget Director of Communications Office of the Minister of Fisheries, Oceans and the Canadian Coast Guard [email protected]

Media Relations Fisheries and Oceans Canada 613-990-7537 [email protected]

Stay connected

• Follow Fisheries and Oceans Canada on  X ,  Facebook ,  Instagram  and  YouTube .
• Follow the Canadian Coast Guard on  X ,  Facebook ,  Instagram  and  YouTube .

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