Long-Lived Trees’ Epigenetic Mutations Serve as a Molecular Clock
Long-Lived Trees’ Epigenetic Mutations Serve as a Molecular Clock

Long-Lived Trees’ Epigenetic Mutations Serve as a Molecular Clock

Cells found in different branches of a tree have different patterns of DNA methylation, changes in which accumulate over time.

Jef Akst
Jef Akst
Mar 1, 2021

ABOVE: David Braun from BraunArborCare climbs the tree in Hood River, Oregon, used in the study.
BOB SCHMITZ

EDITOR’S CHOICE IN GENETICS & GENOMICS

The paper
B.T. Hofmeister et al., “A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa,” Genome Biol, 21:259, 2020.

Like animals, plants can accumulate alterations in their epigenomes—the pattern of epigenetic marks on their DNA. So far, researchers have only examined the epigenomes of short-lived annual plant species. As a result, it has been impossible to tell if those mutations arise throughout development or just during gamete production, as many in the field assumed, explain long-time collaborators Frank Johannes of the Technical University of Munich’s Institute for Advanced Study (TUM-IAS) and the University of Georgia’s Bob Schmitz, who has a fellowship at TUM-IAS. 

To understand how DNA methylation changed over time in long-lived species, Johannes, Schmitz, and their colleagues decided to investigate the epigenome of a 330-year-old poplar (Populus trichocarpa) near Mt. Hood, Oregon. The team first measured the diameters of the base and tip of eight tree branches and took samples from most of those locations to count the concentric rings that reflect each branch’s age. The researchers then analyzed leaf samples from each branch for variations in DNA methylation and found that the number of epimutations correlated with age. “Over the course of 300 years of cell divisions, you can really find very clear accumulation of these sites over time,” says Schmitz. 

Comparing the epigenomes of cells found in different branches of a 330-year-old tree, researchers estimate its epimutation rate to be 10,000 to 100,000 times faster than its genetic mutation rate.
Genome Biol, 21:259, 2020

The study is an important starting point for understanding how the epigenome changes over time in long-lived plant species, says West Virginia University forest geneticist Stephen DiFazio. “That stuff is novel, and it’s really important, because that’s a dimension of genomic variation that is not well understood currently,” he says. “The paper raised probably more questions than it answered, but that’s to be expected for something that’s kind of a breakthrough first step.” 

Johannes and Schmitz’s team also created a software package that researchers can use to estimate epimutation rates to calculate the age of trees. “In a sense, these epimutation clocks are better than genetic clocks in some settings,” says Johannes. Because epimutations are happening 10,000 to 100,000 times faster than genetic mutations, it provides a finer scale of resolution. “We get a lot more events happening so the clock ticks faster.”

Correction (March 2): This story has been updated from its original version to correct the species name from Populus tremuloides to Populus trichocarpaThe Scientist regrets the error.