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.
Pilot work in Minnesota has shown that starry stonewort populations and growth patterns of can vary between years and between lakes in different locations. These patterns suggest that how starry stonewort invades a lake could be influenced by climatological factors such as ice-out date, growing season length, and average water temperature. If this is the case, then developing effective management strategies for starry stonewort requires a deeper and more specific understanding of how climate change will influence the invasion dynamics of the species.
The project includes:
- An empirical study of starry stonewort invasion dynamics in nine lakes across latitudinal gradients in Wisconsin, Minnesota, and Indiana.
- Interviews with AIS managers and decision-makers in Wiscnsin, Minnesota and Indiana to examine invasive species management perceptions and preferences as they relate to starry stonewort.
- Modeling starry stonewort invasion patterns under a range of climate and management scenarios.
This project will provide practical information on the ecology of starry stonewort, a summary of current stakeholder preferences around starry stonewort management, as well as an evaluation of optimal management strategies.
The study is one component of a larger research project that is funded by the Prepared for Environmental Change Grand Challenge initiative administered by the Environmental Resilience Institute at Indiana University.