Genome Jamboree Brings Scientists from Around the World to Wooster

Researchers and educators work to correct and re-annotate the Paramecium Genome database

Paramecium tetraurelia

WOOSTER, Ohio - As thousands of area residents prepared to celebrate Wooster's Bicentennial parade earlier this month, a small group of scientists was wrapping up a much less conspicuous but arguably more ambitious undertaking at The College of Wooster. Eighteen researchers and educators from around the world, including Turkey, France, and Japan, descended on Wooster's campus for the inaugural Paramecium Genome Workshop and Annotation Jamboree, June 30-July 2.

Sound like fun? Maybe not to the average Joe, but to these scientists, it was both enjoyable and educational. The purpose of the workshop was to assemble members of the genome community and show them how to correct and re-annotate inaccurate information in the existing database. "The computer looks at a variety of sequences, but it often makes errors," said Dean Fraga, associate professor of biology at Wooster and host for the workshop. "One common type of error is what can be called an 'assembly error, and these can be readily identified and corrected by properly trained people, including students."

Why so much interest in such a tiny organism? Well, it turns out that these single-celled organisms can tell us a lot about ourselves, according to Fraga. "Paramecium can provide information about how life evolved and research in Paramecium has unearthed several fundamental concepts about how life functions," he said. "It has a lot in common with us, and by understanding how it functions, we can learn more about ourselves."

Linda Sperling, director of the Paramecium genome project, came from France to lead the workshop, which was attended by scientists from Princeton, Purdue, Indiana, the Ohio Agricultural Research and Development Center, and elsewhere. In her opening address, Sperling described the genome and explained how it is represented in the database. Scott Cain of Cold Spring Harbor Laboratory in New York gave an overview of the Generic Model Organisms Database (GMOD) and the various tools available for researchers to develop their own genome databases. Fraga spoke about RNAi (a mechanism that inhibits gene expression by hindering the transcription of specific genes) and how it can be used in the classroom to generate functional data that can be included in the Paramecium database. Wei-Jen Chang of Hamilton College explained how the Apollo software package could be used in the classroom to correct the errors and add useful information to the database.

After the presentations, participants used Apollo to re-annotate selected genes that had been incorrectly annotated by automated systems, according to Fraga. On the final day of the workshop, seven scaffolds (large groups of contiguous genes in the genome) were examined and re-annotated, correcting any mistakes that were found and verifying that other genes were properly identified by the computer.

The significance of the workshop at Wooster was that the participants essentially volunteered their time to correct the information that was in the database. "There is an esprit de corps among this group of researchers," said Fraga. "We don't have as much funding as the Human Genome Project, for example, to hire a team of annotators dedicated to this single purpose. But researchers in the field were very willing to come in and assist, much to our delight.

"We're hoping that this type of approach can serve as a model for others in the future about how to adapt a problem in genomic science, correcting the huge number of genes incorrectly annotated by the automated systems, for use in the classroom to help students appreciate how genomes are characterized," added Fraga. "Students will learn about genes, gene structure and genomes, and the research community will have a properly annotated genome. Our long-term goal is to work with researchers, educators, and students to correct and re-annotate the entire database."