Zebra mussels (Dreissena polymorpha are considered by many to be the most economically and ecologically damaging freshwater invasive species in Minnesota, and throughout their invaded range across the U.S. and Canada, Europe, and the British Isles. These researchers collaborate with with the University of Minnesota Genomics Center on de novo sequencing of the zebra mussel genome from Illumina short reads and PacBio long reads. RIS analysts at MSI and several other partners have completed and scaffolded the assembly to the level of chromosomes. Because zebra mussels diverged hundreds of millions of years ago from the most closely related molluscs with reference genomes, these researchers are manually annotating several set of genes that automated methods fail to resolve. RNA-sequencing data from selected tissues, and comparative and functional genomic analysis are applied to genes that are likely to control invasive success, and to identify potential target genes for genetic biocontrol and other management efforts.
The researchers also use population genetics and genomics to study pathways of spread in Minnesota and the surrounding Great Lakes region to help advise spread prevention. They have generated SNP genotypes for thousands of mussels using genotyping by sequencing. This involves Illumina NextSeq sequencing of reduced-representation DNA libraries prepared from restriction digested genomic DNA, using protocols that we developed and refined for populations in our region. A large amount of next generation sequencing data needs to be stored and accessed through MSI as the researchers continue to analyze genome sequences and SNP genotypes.