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

While our first focus to reduce zebra mussel spread and impacts in Minnesota should be on well-informed inspection and decontamination programs, prevention cannot stop all new invasions, particularly in Minnesota, with >11,000 lakes and > 4,650 boat ramps (including DNR, local, and private). Phase II therefore also includes a substantial focus on researching zebra mussel control options. 

While several researchers are pursuing options related to chemical pesticides and biological controls, including microorganisms and parasites, this Phase II project focuses on rapidly growing genetic biocontrol technologies. This includes gene silencing by RNA-interference (or RNAi) as well as genome editing using CRISPR/Cas9 systems that have potential for application to both zebra and quagga mussels. The first step for these technologies is finding target genes that control biological weak points.

In Phase II, we will lay the groundwork for potential genetic biocontrol by completing the following:

  • Producing the first-ever complete sequence of the zebra mussel genome
  • Developing a Dreissenid Mussel Genome Collaborative (DMGC) to generate strategies for applying genetic technologies to zebra and quagga mussel biocontrol
  • Analyzing the zebra mussel genome (and “transcriptomes” of expressed genes) to find genes that could be targets for these technologies.


All required samples have been collected and genotyped using Sequence-Based Genotyping. The zebra mussel genome has been sequenced and a high-quality assembly has been prepared. Researchers then scaffolded the assembly to map the sequences to chromosomes. We measured expression of genes in tissues that control shell formation, byssal thread attachment, and survival in high temperatures—each are strong candidates for target genes. The results include a publicly accessible genome: a powerful tool for invasion biology and biocontrol researchers in Minnesota and worldwide.

This is the first complete genome from zebra or quagga mussels; among the world’s worst aquatic invasive species. It is of very high quality, providing a powerful resource for basic biology and for development of biotechnologies—for researchers in Minnesota, and across the invaded ranges in North America and Europe and the native range in Eurasia. For managers, its significance is probably greatest in the area of biocontrol research and development, for which a genome sequence is a necessary basic resource.

Project manager: Mike McCartney

Funded by: Environment and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources

Project state date: 2017

Project end date: 2018