Description;
Ancient DNA switches found in plants 400 million years later.When we think of evolution, gradual evolutionary change comes to mind: dinosaurs turning into birds, ancient forests transforming into the world around us. But all this upheaval hides a more subtle story, one that takes place at the level of plant DNA. It is a story of conservation, persistence, and molecular information embedded in ancestral genomes that have survived for millions of years For decades, biologists have puzzled over a strange paradox. Genes themselves often remain remarkably similar across species, even after those species diverged years ago. Yet the DNA that controls when those genes are turned on or off, so-called regulatory DNA, has seemed far less predictable. Rapid DNA turnover, genome duplications, and rearrangements seem to erase the trail. Many have wondered whether plants have conserved regulatory sequences all Now, a breakthrough has rewritten that narrative. In a large study published in Science, researchers at Cold Spring Harbor Laboratory (CSHL) and collaborators around the world discovered more than 2.3 million conserved noncoding sequences (CNSs), including more than 3,000 ancestral angiosperms, in 284 plant species spanning 284 million years. These ancient sequences weren't just relics. They clustered near developmental regulator genes like the HOMEOBOX family, and when researchers changed them, the plants showed dramatic changes in growth and shape. In other words, these hidden switches are essentials for life. Using a new computational tool called Conservatory, the team tracked these sequences across 284 species. Some of these sequences are incredibly old, dating back more than 400 million years, long before flowering plants appeared. The key to the study lies in careful analysis. They didn’t scan the genome extensively. Instead, they examined gene clusters at a fine scale and compared their arrangements on a smaller scale, from one ancestor to another, across hundreds of species. This revealed conserved elements that older methods had missed. CSHL postdoc Anat Handelman, a co-first author, acknowledged that the team was stunned: "Isolating and genetically modifying these CNSs confirmed that they are essential for developmental function.The study also revealed three guiding principles for CNS evolution in plants. First, the importance of sequence: Even if the distance changes, the sequence along the chromosome remains constant. Second, new links are formed: When genomes rearrange, CNSs can be linked to different genes. And third, old guides endure: Ancient CNSs often persist after gene duplication, fueling the evolution of new traits. Scientists successfully create beautiful glowing plants."We didn't just find CNSs," explained Zachary Lippman of CSHL. "We found that new regulatory sequences often come from old ones, which are rearranged after replication. That's how novelty emerges."This conservatory project enables scientists to access a comprehensive atlas of plant regulatory DNA spanning crops and their wild ancestors. For plant biologists and breeders, it is more than a scholarly treasure trove. It is a practical tool. Understanding how regulatory DNA is conserved and reshaped could help crops withstand drought, improve yields, and address food shortages. But the implications extend further. As Lippman said, “This is a new window into the evolution of life over many years and a new opportunity to engineer or improve crop traits more efficiently.”Most of us have heard of deep space, the vast expanse of space beyond Earth, connected to the stars. But scientists also explore something equally mysterious: deep time.Deep time is not just an idea, it is a living record embedded in the DNA of plants. Decoding these ancient regulatory sequences allows scientists to solve a puzzle that has been going on for decades. It also opens up new avenues for agriculture and reveals new chapters in the story of life itself.Journal Reference:Kirk Amundsen, Anat Handelman, Daniel Seren, et al. A deep temporal view of plant cis regulatory sequence evolution. Science. DOI: 10.1126/science.adt8983
