Major milestone reached in effort to sequence the draft zebra mussel genome
The Minnesota Aquatic Invasive Species Research Center is partnering with the U’s Genomics Center to do something that’s never been done before: sequence the zebra mussel genome.
This work, which kicked off in the fall, recently reached an important milestone: the Genomics Center completed the first step of generating sequences from billions of short fragments of the DNA, which were originally extracted from a single, 4-centimeter long zebra mussel.
This process, done using a technology called “Illumina paired-end sequencing,” generated roughly 1.5 billion high-quality chunks of data – or “reads” as they are called – an excellent outcome, according to project lead Dr. Michael McCartney. On the downside, however, was the finding that zebra mussels appear to have DNA sequences that are repeated over and over in their genomes. This was the case when another bivalve mollusk, the Pacific oyster, was sequenced, and it presents a challenge when it comes to assembling the reads into a complete genome.
To overcome the problems that repetitive DNA pose, researchers at the Genomics Center are also using a technology that generates sequences from fewer, but longer, fragments of DNA. The information learned from this work will be analyzed by bioinformatics experts at the Supercomputing Institute, thanks to recently received funding from the U’s Informatics Institute. Together, this diverse group of researchers hopes to generate a full-length draft of the genome within several months.
By genetically “typing” hundreds of mussels according to thousands of DNA markers, and by mapping these markers in reference to the draft genome, researchers Michael McCartney and Sophie Mallez will be able to determine the origin of the mussels in prominent lakes that are already infested, such as Mille Lacs and Minnetonka. They also hope to identify important routes of spread that can be targeted for prevention. In the future, with additional funding and partnerships, this research could also reveal genetic weaknesses in the species that could be targeted or manipulated for control efforts.
