Image: A project to decode the genome of aspen trees has revealed a new wrinkle in how chromosomes are constructed—and it may have larger evolutionary implications, according to researchers in the Tsai lab at the University of Georgia. Using new, high-powered sequencing and assembly technologies, Ran Zhou, a postdoctoral associate in the lab of C.J. Tsai, a professor in Plant Biology and the Warnell School of Forestry and Natural Resources, was able to identify hundreds of thousands of DNA pieces that are included in the genome, called satellite DNA. But Zhou took it one step further, identifying their unusual abundances and organizations in multiple chromosomes. Zhou’s work to identify and classify these repetitive sequences sheds new light on satellite DNA, challenging the conventional theory that large satellite DNAs are primarily found in centromere, or the central portion of a spindly, X-shaped chromosome. The study was published in November 2023 in a special “Resource” issue of The Plant Journal and made the cover. “When you see people draw a chromosome, they draw an X and the centromere is the connector,” said Zhou, who began the project in 2021 to analyze millions of strings of DNA taken from a hybrid aspen (Populus tremula x P. alba clone “717”) and sequenced by the U.S. Department of Energy’s Joint Genome Institute and the HudsonAlpha Institute for Biotechnology. The conventional theory was that the satellite DNA was primarily centromere parts—but previous iterations of the genome project, which began in 2016, couldn’t stitch the highly similar DNA pieces together in the right order or the right place of the chromosomes to assess this. More than building blocks, Satellite DNA can be found in DNA across all life forms, said C.J. Tsai, the Winfred N. "Hank" Haynes Professor and Georgia Research Alliance Eminent Scholar whose lab conducted the study. “Sometimes it’s here and sometimes it’s here,” said Tsai, pointing to different places along an illustration of DNA. “We thought it might be random, but it might be evolution.” “We thought [the satellite DNA] might be conserved just like most genes, but when we checked more widely through the population—not just aspens but other cottonwoods and balsam poplars—it’s only present in the aspen species,” said Zhou. “All the other species don’t have this type of satellite DNA, but yet they are so similar. So that’s the exciting finding—we might have found something that is evolutionary important,” said Tsai. “Because if they weren’t evolutionarily important, they probably would be purged.” A detailed approach - Sequencing the aspen genome was a years-long process, said Tsai, but it’s not necessarily groundbreaking. Her lab, which investigates tree survival through genetic manipulation such as CRISPR, decided to pursue the project after running into hiccups on past projects. It was clear, she said, that the DNA for cottonwoods and poplars, while similar to aspen, held some differences. While in some instances her lab could resolve the differences in DNA, some remained a puzzle. “When we talk about precision medicine, it’s different between you or me—little bits of difference can really complicate an analysis,” she said. “If you look for gene similarities you will find them, but if you don’t have the real genome, you will never find the differences.” She teamed up with Bob Schmitz, UGA Foundation Professor in Plant Sciences, and Jeremy Schmatz of HudsonAlpha, and together they secured funding from the National Science Foundation and the Department of Energy to sequence the genome. While the team obtained a draft genome a few years ago, it had many gaps. Tsai wondered if advances in technology could push their information even further. “The sequencing technology had made another breakthrough, so we decided to sequence more. … It truly improved the quality of the genome,” said Tsai. “Previously we had to make a scientific guess with software algorithms to string DNA sequence into long segments. This could be erroneous when you run into many similar pieces like satellite DNA,” added Zhou. “But now we can essentially read through megabases of DNA in the genome to directly determine how many copies are there.” The purpose of satellite DNA isn’t fully understood, but as Tsai noted, DNA does more than hold cell building blocks—it also holds “on” and “off” switches to certain biological processes. If a string of DNA were the road map, what if the satellite DNA were the turns you took along the way? Zhou’s work, Tsai noted, promotes the potential of satellite DNA from a background character to a supporting role. This article is a shortened version of an article first published by the UGA Warnell School of Forestry and Natural Resources.
