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Decoding of aspen tree genome reveals new satellite DNA

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 at the University of Georgia.


Using new, high-powered sequencing and assembly technologies, Ran Zhou, a postdoctoral associate in the UGA 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.scientist holding flask


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 recently published online and will appear in a special “Resource” issue of The Plant Journal later this year.


 “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.


With the improved and highly contiguous genome, Zhou saw millions of satellite repeats from different places across that X shape, rather than near the centromere.


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.”


That’s because, as Zhou analyzed the aspen genome, he was able to align it closely with that of cottonwood and poplar, two trees in the same genus as aspen. So, it would make sense that the three varieties of trees would share DNA. But when you add the satellite DNA to the mix, suddenly aspen’s genome looks considerably different.


“We thought it 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. 


Seeing the difference in the aspen genome created by the satellite DNA elevates the scientists’ line of questions, said Tsai. It’s easy to consider satellite DNA as “junk,” as if it’s holdover pieces from a bygone era. But when you consider that aspen trees don’t hybridize with cottonwoods or poplars—trees that, for the most part, could be considered close relatives—it puts this satellite DNA into a new light. 


“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.”


It was in this review of the updated genome sequence, provided by the Joint Genome Institute, that Zhou realized the abundance and variety of satellite DNA. Its purpose isn’t fully understood, although, 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. 


“Ran’s discovery for the aspen-specific satellite DNA actually elevates our question to like 30,000 feet. It opens up evolutionary questions that, if you ask us now, we don’t know the answers to,” she said. “But we know aspens don’t get along with cottonwoods—they are not compatible but from the same genus. And we found something that is specific to aspen. We might be on to something that might explain their reproductive isolation.”

This study was recently published in a special "Resource" issue of The Plant Journal as the featured cover story.


Winfred N. "Hank" Haynes Professor, Georgia Research Alliance Eminent Scholar

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