Scientists uncover 300 million year old DNA code hidden in plant genomes
An international team of scientists has identified about 2.3 million ancestral DNA sequences that function as hidden genetic instructions across the plant kingdom. Some of these regulatory elements have remained conserved for nearly 300 million years of evolution. The findings, published March 12 in the journal Science, represent the most comprehensive map yet of conserved regulatory DNA in plants and could help researchers design crops that are more resilient to environmental stress.
For decades, botanists faced a major puzzle. Many plant species grow leaves, stems and flowers using remarkably similar developmental patterns, yet the shared genetic instructions behind these processes were difficult to locate. Unlike animal genomes, where ancient regulatory elements are well documented, plant genomes constantly undergo rearrangement, duplication and structural changes. These processes obscured the regulatory sequences and made them difficult to detect.
To address this challenge, researchers developed a computational tool called Conservatory. The project was led by Professor Idan Efroni of the Hebrew University of Jerusalem, Professor Zachary Lippman of Cold Spring Harbor Laboratory, and Professor Madelaine Bartlett of the University of Cambridge.
Using the new tool, the team analyzed 314 genomes from 284 plant species. Conservatory works by progressively assembling genomic fragments and matching similar sequences across increasingly distant species. This approach allowed scientists to filter out genomic noise that had previously blocked attempts to identify ancient regulatory DNA.
The researchers identified roughly 2.3 million conserved non coding DNA sequences. More than 3,000 of these elements predate the emergence of flowering plants. The oldest regulatory sequences were found clustered near genes that control fundamental aspects of plant structure, especially genes belonging to the HOMEOBOX family.
Experiments confirmed the importance of these ancient elements. When researchers introduced mutations into some of the conserved sequences, the plants developed severe developmental abnormalities. The results showed that these regions are not inactive evolutionary remnants but remain essential for normal plant growth.
The discovery could have direct implications for agriculture and food security. Many crop traits depend not only on genes themselves but also on how those genes are regulated. According to Lippman, the findings provide a new perspective on how plant life evolved and offer a new opportunity to improve crop characteristics more precisely.
The Conservatory database is now publicly available and includes dozens of crop species as well as their wild relatives. Scientists say it could guide precision breeding and synthetic biology strategies aimed at producing drought resistant and higher yielding crops without altering the genes directly. Instead, researchers could modify the regulatory switches that control gene activity.
Efroni noted that despite hundreds of millions of years of genomic reshuffling, the core regulatory logic governing plant development has remained remarkably stable.
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