Most people are familiar with the concept of deep space, but scientists also study something called deep time. Advances in genetics have allowed researchers to trace biological changes farther back in time than ever before. Even with these powerful tools, many questions remain unanswered. A long-standing mystery has puzzled biologists for decades.
Genes and their functions are often surprisingly similar between species, even if those species diverged hundreds of millions of years ago. This pattern appears in both plants and animals. But the same consistency doesn’t seem to apply to DNA, which controls when genes are turned on or turned off. Scientists have struggled to determine whether this type of DNA, known as regulatory DNA, remains conserved within plants over long evolutionary periods. For many years, some researchers suspected that plants had no such protection at all. New findings suggest otherwise.
Discovery of ancient regulatory DNA in plants
Research published in science Research by Cold Spring Harbor Laboratory (CSHL) and collaborators around the world has identified more than 2.3 million regulatory DNA sequences conserved across 314 plant genomes in 284 species. These sequences are known as conserved non-coding sequences (CNS). The team discovered them using a new computational tool called . conservatorywas developed through a collaboration between the laboratories of Idan Efroni at the Hebrew University, Madeleine Bartlett at the Sainsbury Institute at the University of Cambridge, and Zachary Lipman at CSHL.
Some of these central nervous systems appear to be very old. Researchers found evidence that certain sequences originated more than 400 million years ago, when flowering plants diverged from non-flowering ancestors.
Comparison of hundreds of plant genomes
How were scientists able to uncover so many previously hidden regulatory sequences?
The researchers focused on examining the organization and composition of very small groups of genes. 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 missed by previous methods.
CSHL postdoctoral researcher Anat Handelman, co-lead author of the study, said the research team was surprised that many of these regulatory sequences existed unnoticed. “When we took these central nervous systems apart and gene-edited them, we confirmed that the central nervous system is essential for developmental function,” Handelman says.
Three important rules of plant regulatory DNA evolution
The study also revealed three important patterns that help explain how the CNS evolves within plant genomes.
First, although the physical spacing between these sequences can vary, the order of the sequences along the chromosome tends to be consistent. Second, as plant genomes are rearranged during evolution, the CNS may become associated with different genes. Third, the ancient CNS often persists even after genes have been duplicated, making it a major driving force for the evolution of plant genomes and gene families.
“In fact, this was one of the reasons why we couldn’t discover the central nervous system using the same approach used in animals,” Lipman explains. “We not only discovered the CNS using this innovative approach; we found that new regulatory sequences often originate from old CNS that have been modified after gene duplication. This helps explain how new regulatory elements emerge.”
A new atlas for plant biology and crop science
The greenhouse 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 investigate how regulatory DNA has been conserved and reformed throughout plant evolution.
The discovery could prove particularly valuable to crop breeders seeking to address challenges such as drought and food shortages. But the significance of this discovery goes far beyond agriculture. “This is a new window into the evolution of life over many years, and a new opportunity to more efficiently manipulate or fine-tune crop traits,” Lippmann said.
