Transcriptomics in Black carp (Mylopharyngodon piceus)

Invasive carp (silver carp, bighead carp, grass carp, and black carp) are a highly impactful species with high fecundities, and they are currently expanding their ranges throughout the Central United States. These four species are known to avoid the conventional gear used to capture native fish species, and traditional removal methods are highly inefficient at capturing fish when at low abundance. Therefore, new tools are needed for resource managers to manage these invasive species and minimize the risk of them spreading more effectively. The USGS Ecosystems Mission Area Invasive Species Program supports ongoing research in support of the Great Lakes Restoration Initiative to develop and test control technologies for invasive carp, including the invasive molluscivore black carp. This project will sequence a transcriptome from black carp tissues to support the development of target genes for RNA interference (RNAi). A limited number of pesticides are available or in development, although these are toxic chemicals and can have significant non-target effects. Synthetic biology technologies have the potential to effectively target low-abundance populations and be truly species-specific without non-target effects. Several synthetic biology technologies can be considered, and we will use modeling to evaluate the potential of these technologies to exploit natural processes and control invasive carp. One technology that seems to have the most practical application and the most straightforward path forward to implementation is RNA interference. In addition to modeling other technologies, we will develop and evaluate RNA interference control tools for controlling black carp. The transcriptome sequence of black carp is required before any siRNA molecules can be designed, and it will also enable numerous other genetic studies to be initiated. This powerful method is both targeted and untargeted, allowing scientists to detect black carp homologs to known gene networks characterized in model fish species and identify new gene pathways that may be unique to black carp. Sequencing the entire transcriptome increases the chance for success at identifying genes that are essential to black carp physiology and vulnerable to perturbation by RNA interference