USC Aiken biology students use cutting-edge technology to sequence DNA of the South Carolina state tree

University of South Carolina Aiken Associate Professor Nathan Hancock and his students are using breakthrough technology to decode the DNA sequence of the Sabal palmetto tree through a partnership with the American Campus Tree Genomes (ACTG) Project. In doing so, students can enhance their bioinformatic skills, giving them an advantage in graduate studies and the workforce.

The ACTG Project was created by Alex Harkess, a faculty investigator with the Hudson Alpha Institute for Biotechnology in Huntsville, Alabama. Like Hancock, other professors around the country are partners on the project, decoding species such as the Auburn oak in Alabama and the Anjou pear and Cosmic Crisp apple in Washington.

Hancock says, "I thought that the Sabal palmetto was a perfect project for South Carolina students because of its important role in the history of our state. Despite the cultural and historical significance, little is known about the fundamental genetic makeup of this beloved native species."

South Carolina is nicknamed the Palmetto State because of the role these trees played in fighting the British during the Revolutionary War. The original Fort Moultrie was made of palmetto logs because of their ability to absorb the shock of incoming cannon fire, helping the Patriots defeat the British.

After obtaining a permit from the National Park System, Hancock collected leaf tissue from a palmetto at Fort Moultrie. The sample was sent to HudsonAlpha where the DNA will be purified and sequenced. When the raw data is returned to USC Aiken, Hancock's students will use a sequence analysis pipeline to assemble it into chromosomes. They will compare their findings to the coconut, date palm, and oil palm genomes to identify unique traits of the Sabal palmetto species.

Hancock says, "We want to compare these species and see how they grow and adapt to different environments. This will be a great student project because it will give them the DNA analysis skills needed to succeed in a broad range of biological sciences."

The ACTG Project is funded by a grant awarded to Harkess from the National Science Foundation, which provides for DNA sequencing equipment. On a local level, Hancock raised funds allowing his students to access cutting-edge cloud computing software needed to assemble the sequences into chromosomes and identify the genes.

Harkess says, "This initiative was founded on the idea that iconic trees can serve as a gateway for students to interact with the latest genome sequencing technologies, and put them into collaborative cohorts where they authentically assemble, analyze, and publish these genomes in high-quality journals. In doing so, we not only immortalize these trees, but we create opportunities for students to advance their careers with new bioinformatic skills and reduce the barriers that have prevented some students from entering and staying in STEM fields."

By next summer, Hancock hopes to have findings ready for publication and submission to scientific journals. If funding allows, he plans to place a plaque at Fort Moultrie marking the tree that was sequenced for the project.

He says, "This project demonstrates something significant that our campus is doing for the state of South Carolina and also for our students. Having experience in sequence analysis will give them an advantage both in industry and in applying for graduate studies. In biological sciences, analyzing DNA sequence is such a big part of what we do."

Support the Palmetto Project

More than $6,000 has been raised for the Palmetto Project from alumni, faculty, and staff at USC Aiken and donors in the greater community. Please consider joining this effort to support student research efforts! Donations may be made online or by mailing a check payable to Aiken Partnership to 471 University Parkway, Aiken, SC 29801. Please note "Palmetto Project" in the memo line for check donations.