黑料吃瓜资源

You鈥檝e heard of deep space, but what about deep time? Today鈥檚 geneticists and evolutionary biologists can extend their investigations further back in time than ever imagined. Still, many mysteries remain. One has vexed biologists for decades. In both plants and animals, gene sequences and functions are often conserved across species over hundreds of millions of years. However, this breaks down when comparing DNA that controls gene activity. And no one has been able to pin down whether this 鈥渞egulatory DNA鈥� is conserved in plants at all. It got to the point where many thought such conservation simply does not exist. Think again.

A new study published in Science by 黑料吃瓜资源 (CSHL) and international collaborators reveals the discovery of more than 2.3 million regulatory DNA sequences conserved across 314 plant genomes from 284 species. These 鈥渃onserved non-coding sequences鈥� (CNSs) were identified using a new computational tool called , developed between the labs of Idan Efroni at Hebrew University, Madelaine Bartlett at Sainsbury Laboratory Cambridge University, and Zachary Lippman at CSHL. Amazingly, the team found that some of these CNSs date back to before flowering plants split from their non-flowering ancestors over 400 million years ago.

Talk about deep time! How did their approach yield such a bounty of discovery?

The key was to examine and compare the order and makeup of all gene groups on a tiny scale, from one ancestor to the next, across hundreds of genomes. CSHL postdoc Anat Hendelman, a co-first author of the study, was amazed to see how many of the CNSs they found have been around all along. 鈥淧icking apart and genetically editing these CNSs confirmed they鈥檙e essential for developmental function,鈥� Hendelman says.

The team鈥檚 research revealed three core principles of CNS evolution in plants. First, though the spacing of these sequences varies, the order in which they appear on the chromosome is conserved. Second, when genomes get rearranged, CNSs start associating with different genes. Finally, ancient CNSs tend to persist when genes become duplicated, a crucial feature of plant genome and gene family evolution.

鈥淭his was actually one reason CNSs could not be discovered using the same approaches used in animals,鈥� Lippman explains. 鈥淲e didn鈥檛 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.鈥�

With the Conservatory project, plant biologists like CSHL project collaborator David Jackson can now access what the researchers call a 鈥渃omprehensive atlas of regulatory conservation across plants, including dozens of crop species and their wild ancestors.鈥�

That鈥檚 a huge resource for plant breeders looking to meet major challenges, such as droughts and food scarcity. But the implications go far beyond agriculture. As Lippman puts it, 鈥淚t鈥檚 a new lens on the evolution of life across eons and will make genome editing far more efficient for engineering crop traits.鈥�

Written by: Samuel Diamond, Senior Communications Strategist | [email protected] | 516-367-5055

Funding

Binational Science Foundation, Israeli Science Foundation, Howard Hughes Medical Institute, National Science Foundation Plant Genome Research Program, USDA National Institute of Food and Agriculture, Gatsby Foundation

Citation

Amundson,听K.R.,听Hendelman, A.,听et al., 鈥�A deep-time landscape of plant cis-regulatory sequence evolution鈥�,听Science,听March听12,听2026. DOI:听

Core Facilites

鈥淭丑别 Sequencing Technologies and Analysis Shared Resource provides access to an array of high throughput Next Generation Sequencing (NGS) technologies. We offer cutting-edge technology alongside convenient in-house services for a broad range of genetic analysis.鈥� 鈥� NGS Director Sara Goodwin, Ph.D.