Skate Genome Workshop Held at the MDI Biological Laboratory

Skate Genome WorkshopNearly two dozen scientists and students from across the Northeast gathered at the Mount Desert Island Biological Laboratory last week (Oct. 12-15) to identify genes in the little skate, an ancient fish similar to a sting ray that is able to regrow its limbs as an adult. This effort to identify all of the genes in the skate is part of a collaborative project initiated by the IDeA Networks of Biomedical Research Excellence or INBREs in five northeastern states, including Maine. INBREs exist to boost the competitiveness of states in which the aggregate success rates for federal research grants has been low, and are funded by the National Center for Research Resources at the National Institutes of Health (NIH).

“The skate genome project provides an ideal opportunity for students to participate in a scientific project that is literally charting new territory,” says Ben King, a staff scientist at the MDI Biological Laboratory and co-leader of the project. “Annotating the genome, or figuring out what parts play which role, requires an enormous effort that is best achieved through collaboration. It’s exciting to have so many INBRE institutions working together.”

With 3.4 billion base pairs or “letters” in the genetic code, the skate genome is slightly larger than the human genome. As the skate is believed to have evolved 450 million years ago, a genetic “road map” of this ancient creature will offer new insight into evolution and reveal which genes have been retained or “conserved” over those millions of years.

The skate genome will also be an important tool for scientists at the MDI Biological Laboratory who are studying how skates are able to grow new limbs as adults after an injury. By comparing genes in the skate with those known to be involved in embryonic development and regeneration in other species, MDI Biological Laboratory scientists can learn more about why humans and other vertebrates have lost the ability to regenerate their limbs.

The massive sequencing effort draws on expertise in all five of the collaborating states. The original genetic material was obtained at MDIBL. Technicians and faculty at the University of Delaware have been determining the actual sequences, using pieces of skate DNA. The resulting data is analyzed at the MDI Biological Laboratory and the University of Vermont. The annotation is taking place in Maine, Delaware, Rhode Island, Vermont, and New Hampshire, and will provide opportunities for follow-up research projects for years to come.

This is the second of three planned annotation workshops. The workshops offer training and opportunities for faculty and students to work together. “We’re hoping that the faculty and student pairs that are learning together here at the workshop will start their own research projects based on the skate genome,” says Ben King.

The sequencing effort relies on the North East Cyberinfrastructure Consortium, which is building and connecting the infrastructure required to share the huge data sets generated by the sequencing project. The Consortium is funded by the National Science Foundation and NIH and has received stimulus funds to complete a dedicated fiber optic network linking research institutions in Vermont, Maine, New Hampshire, Delaware, and Rhode Island.

Stimulus funds from the American Recovery and Reinvestment Act are also supporting the skate genome project through the INBRE program. The Maine INBRE links the MDI Biological Laboratory, as lead institution, with The Jackson Laboratory and eleven Maine colleges and universities.