Most people are familiar with the idea of deep space, but scientists also study something called deep time. Advances in genetics now allow researchers to trace biological changes far deeper into the past than previously possible. Even with these powerful tools, many questions remain unanswered. One long standing puzzle has challenged biologists for decades.
Genes and their functions often stay remarkably similar across species, even when those species diverged hundreds of millions of years ago. This pattern appears in both plants and animals. However, the same consistency does not seem to apply to the DNA that controls when genes turn on or off. Scientists have struggled to determine whether this type of DNA, known as regulatory DNA, remains conserved in plants over long evolutionary periods. For many years, some researchers believed that such conservation might not exist in plants at all. New findings suggest otherwise.
Discovery of Ancient Regulatory DNA in Plants
A study published in Science by Cold Spring Harbor Laboratory (CSHL) and collaborators around the world has identified more than 2.3 million regulatory DNA sequences that remain conserved across 314 plant genomes from 284 species. These sequences are known as conserved non-coding sequences (CNSs). The team located them using a new computational tool called Conservatory , developed through collaboration among the laboratories of Idan Efroni at Hebrew University, Madelaine Bartlett at Sainsbury Laboratory Cambridge University, and Zachary Lippman at CSHL.
Some of these CNSs appear to be extremely ancient. The researchers found evidence that certain sequences originated before flowering plants diverged from their non-flowering ancestors more than 400 million years ago.
Comparing Hundreds of Plant Genomes
How were scientists able to uncover such a large number of previously hidden regulatory sequences?
The researchers focused on examining the organization and composition of gene groups at a very small scale. By comparing how these gene clusters are arranged across hundreds of plant genomes and tracing their patterns from ancestral species to modern plants, they were able to detect conserved elements that earlier methods had missed.
CSHL postdoc Anat Hendelman, a co-first author of the study, said the team was surprised by how many of these regulatory sequences had existed unnoticed. "Picking apart and genetically editing these CNSs confirmed they're essential for developmental function," Hendelman says.
Three Key Rules of Plant Regulatory DNA Evolution
The study also revealed three important patterns that help explain how CNSs evolve in plant genomes.
First, even though the physical spacing between these sequences can change, their order along the chromosome tends to stay consistent. Second, when plant genomes are rearranged during evolution, CNSs may become linked to different genes. Third, ancient CNSs often remain present after genes are duplicated, which is a major driver of plant genome and gene family evolution.
"This was actually one reason CNSs could not be discovered using the same approaches used in animals," Lippman explains. "We didn't just find CNSs using this innovative approach. We found that new regulatory sequences often come from old CNSs that were modified after gene duplication. This helps explain how novel regulatory elements emerge."
A New Atlas for Plant Biology and Crop Science
The Conservatory project has created what researchers describe as a "comprehensive atlas of regulatory conservation across plants, including dozens of crop species and their wild ancestors." Plant biologists such as CSHL collaborator David Jackson can now use this resource to explore how regulatory DNA has been preserved and reshaped across plant evolution.
The findings may prove especially valuable for crop breeders who are trying to address challenges such as drought and food shortages. Yet the importance of the discovery extends well beyond agriculture. As Lippman puts it, "It's a new window into the evolution of life across eons and a new opportunity to more efficiently engineer or fine-tune crop traits."
