Catching Yellowtail Fish Genome With Big Data

TACC Podcasts show

Summary: Scientists have used big data to catch a big fish genome. Researchers assembled and annotated for the first time the genome of Seriola dorsalis, also known as California Yellowtail, a fish of high value to the sashimi, or raw seafood industry. The science team members were from the U.S. National Marine Fisheries Service, Iowa State University, and the Instituto Politécnico Nacional in Mexico. They published their results January of 2018 in the journal BMC Genomics. Assembling and annotating a genome is like building a three dimensional jigsaw puzzle, and the Seriola dorsalis genome had 685 million pieces - its base pairs of DNA - to put together. The researchers were awarded computational allocations from XSEDE, the eXtreme Science and Engineering Discovery Environment funded by the National Science Foundation. That gave them access to the Blacklight system at the Pittsburg Supercomputing Center to assemble the Seriola dorsalis genome. XSEDE also allocated use of the Stampede1 supercomputer at the Texas Advanced Computing Center to analyze and annotate the fish genome. What's more, the science team got direct help from workflow experts through the XSEDE Campus Champions program at PSC. Podcast host Jorge Salazar interviews two scientists and co-authors of the first-ever genomics work - Andrew Severin, Facility Manager; and Arun Seetharam, Associate Scientist. They're both at the Genome Informatics Facility of Iowa State University.