That’s the question posed by Jingwei Song, a Ph.D. candidate at the Virginia Institute of Marine Science. He studies how the metabolism of spotted seatrout responds to changes in its natural habitat. To aid in his research, he attended a de novo transcriptome assembly workshop given by the National Center for Genome Analysis Support (NCGAS) and supported by the National Science Foundation in Spring 2019.
Jingwei Song collecting fin clip samples for genetic analysis at Lynnhaven River, Virginia.
A transcriptome is the set of RNA molecules that regulate what cells do and how they respond to their environments. While transcriptomes are always needed, they can be particularly valuable when there is no reference genome available for the species under study. While the spotted seatrout is a popular sports fish, there is not yet a reference genome for it. “The de novo transcriptome assembly workshop greatly reduced the learning curve for my analyses,” said Song. And IU’s compute resources helped him prepare his research in time for presentation. “I couldn’t have gotten my preliminary results in time to present at the American Fisheries Society Meeting without the computing resources provided by NCGAS,” said Song.
I couldn’t have gotten my preliminary results in time to present at the American Fisheries Society Meeting without the computing resources provided by NCGAS.
Song’s research illustrates the versatility of de novo transcription: without requiring a full genome, costs of sequencing are dramatically lower, making it an ideal method for studying non-model species. Working in estuaries and coastal waters along the East Coast, Song extracted genetic information through fin clip samples.Currently, populations are robust, and Song aims to inform fisheries of the environmental stressors they face in habitats spanning from Chesapeake Bay to southern Florida and throughout the Gulf of Mexico.
Spotted seatrout prefer water temperatures between 15-20 C, but since their habitats lie in shallow waters near human activity, this is likely to be impacted by climate change. Previous research indicates that if temperature conditions change drastically, so do fish populations. Song’s initial research into thermal stress suggested that Northern populations, collected in Virginia, have more adaptable metabolisms than their counterparts in South Carolina. By developing an understanding of how seatrout respond to low and high temperature stresses, his research can help fisheries better estimate their resilience.
Bridging the gap between field research and rapidly advancing technology, the free three-day workshop used a pipeline developed by NCGAS that employs four separate assembly tools: Trinity, SOAP de novo, Velvet Oases, and TransABySS, along with multiple kmers. The workshop also taught participants how to combine and curate independent assembly data with Evigene software (developed by IU researcher Don Gilbert). NCGAS Senior Bioinformatician Sheri Sanders, developer of both the pipeline and the course, commented, “In addition to Song’s work, many others are using this workshop to inform their research. At present, six publications have used the workflow taught, two dissertations have used the workflow as a substantial portion of the research, and twelve conference presentations have been given on the material. Overall, 39 authors have publications with this workflow in less than two years.”
More information on upcoming trainings will be available in Spring 2020. The National Center for Genome Analysis Support (NCGAS) is a collaborative project between the lead institution, Indiana University (IU), and the Pittsburgh Supercomputing Center (PSC) at Carnegie Mellon University.
