300 million years of hidden genetic instructions shaping plant evolution revealed

A deep genetic mystery has baffled plant scientists for decades. Although leaves, stems, and flowers develop in strikingly similar ways across many plant species, scientists have struggled to identify the shared DNA instructions that guide their formation. A new study now uncovers this hidden regulatory code and shows that its core has been conserved for 300 million years of plant evolution. Remarkably, these ancient DNA sequences were hidden in plain sight but were obscured by the constant reshuffling and duplication of plant genomes. By uncovering this deep-time blueprint, the research reshapes our understanding of plant evolution, showing how core regulatory logic is preserved and modified to guide the diversity of plant shapes and forms. The findings also carry important implications for agriculture, where fine-tuning gene regulation, rather than altering genes themselves, opens new paths to developing more resilient and productive crops.

The DNA of every organism contains both genes and the instructions that determine when and where those genes are switched on. Genes are relatively easy to recognize, like the corner pieces of a puzzle; they have telltale features that stand out. But the regulatory DNA that controls them is far harder to find. New technologies have enabled scientists to uncover many of these sequences in animals, yet plants have remained a major challenge. For hundreds of millions of years, plants have been rewriting their genomes, duplicating, rearranging, and reshuffling vast stretches of DNA, making them especially complex puzzles to decode.

In a new study published in Science, an international team of researchers has uncovered the regulatory blueprint of plants and revealed a key portion of it that has remained conserved across 300 million years of plant evolution. This collaborative research was led by Prof. Idan Efroni of the Hebrew University of Jerusalem, Prof. Zachary Lippman of Cold Spring Harbor Laboratory, and Prof. Madelaine E. Bartlett of the University of Cambridge, with Dr. Kirk R. Amundson of the University of Massachusetts and Dr. Anat Hendelman from Cold Spring Harbor Laboratory.

In a massive comparative effort, the researchers analyzed the genomes of 284 plant species using a powerful new computational tool called Conservatory. To make sense of these complex genomes, the tool assembles them piece by piece, gradually matching similar sequences across increasingly distant species. Drawing on such a large number of species, the researchers identified approximately 2.3 million conserved regulatory sequences, including more than 3,000 that predate the origin of flowering plants, creating the most comprehensive map to date of conserved regulatory DNA in plants.

The team found that the oldest regulatory elements cluster near genes that control plant body architecture. When conserved sequences near some of these genes, from the HOMEOBOX family, were experimentally mutated, plants developed severe abnormalities, demonstrating that these ancient regulatory codes are not evolutionary relics but remain essential today.

The study also reveals fundamental principles of regulatory code evolution in plants: while the spacing between regulatory elements may change, their order is often preserved; chromosomal rearrangements can forge new regulatory partnerships; and ancient elements are preferentially retained after gene duplication, even as some evolve into lineage-specific innovations.

“This study provides a deep-time landscape of plant regulatory sequence evolution,” said Prof. Idan Efroni of Hebrew University. “For decades, we’ve known that developmental gene function is remarkably conserved across plant evolution, but the regulatory sequences controlling those genes seemed to vanish in the noise of genomic change. By developing Conservatory, we were able to recover these hidden instructions and show that, despite hundreds of millions of years of genome reshuffling, the core regulatory logic of plant development has endured. At the same time, our findings show how evolution reshapes, duplicates, and builds on these ancient regulatory instructions to generate the extraordinary diversity of plant forms we see today.”

Beyond illuminating how complex life evolves, the findings carry significant implications for agriculture. Many crop traits depend not only on genes themselves, but on how those genes are regulated. Understanding this deeply conserved regulatory architecture may open new avenues for precision breeding, synthetic biology, and the development of more resilient crops in a changing climate.

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