Instrumentation that can sequence the entire genome of an organism is now available on the South Dakota State University campus, thanks to funding from National Science Foundation, the South Dakota Agricultural Experiment Station, SDSU Office of Information Technology and South Dakota’s BioSystems Networks and Translational Research (BioSNTR) Center.
“Having a sequencing center in South Dakota allows researchers to rapidly acquire genomic data, conduct bioinformatics analyses and then refine their experimental designs,” said BioSNTR director Adam Hoppe.
“High-throughput genome sequencing is not an option anymore—this is something researchers have to do to get funded,” said Department of Agronomy, Horticulture and Plant Science associate professor Jose Gonzalez, who led the team that secured funding.
Gonzalez and assistant professor Sunish Sehgal and associate professor Senthil Subramanian as well as biology and microbiology professor Heike Bucking were awarded a three-year, nearly $350,000 NSF equipment grant in fall 2015. The South Dakota Agricultural Experiment Station and the SDSU Office of Information Technology provided an additional 30 percent in matching funds.
Gonzalez oversees the genome sequencing laboratory at the Young Brothers Seed Technology Laboratory, which houses the Illumina NexSeq 500 nucleic acid sequencer along with accompanying instrumentation to prepare samples.
The equipment was selected based on the amount of output that a typical research project needs, he explained. The machine has the capacity to do one or two human genomes in a single run, with an estimated run time of 30 hours.
The lab offers fee-based sequencing services to researchers at universities and biotechnology firms and has a fulltime technician to prepare samples and do the sequencing Estimates can be requested through https://www.sdstate.edu/genomics-sequencing-facility.
“We can sequence DNA or RNA,” he explained, noting that there is more demand for the RNA sequencing option. “RNA represents all of the genes that are being expressed at any given point in time and in any given tissue—the working machinery.”
For example, a researcher can grow one plant in normal soil and another in high salinity soil and then look at the differences in gene expression between the two plants. “You might have only a few hundred genes differentially expressed—some are the cause of the difference, while others are the effect of that difference,” he explained. “That gives you a good point from which to start.”
Researchers then combine their findings with other evidence or data to get a better understanding of what’s happening.