Across the vast tapestry of life, genes often retain similar functions even among species that separated hundreds of millions of years ago. This trend holds true for both plants and animals, yet the same cannot be said for the regulatory DNA that governs gene expression. For years, scientists have debated whether this regulatory DNA remains conserved in plants over extensive evolutionary timelines. Recent discoveries are shifting this narrative.
Uncovering Ancient Regulatory DNA
A groundbreaking study published in Science by Cold Spring Harbor Laboratory (CSHL) and its global collaborators has identified over 2.3 million regulatory DNA sequences conserved across 314 plant genomes representing 284 species. These sequences, termed conserved non-coding sequences (CNSs), were uncovered using an innovative computational tool called Conservatory. This tool was developed through a collaboration involving Idan Efroni from Hebrew University, Madelaine Bartlett from Sainsbury Laboratory Cambridge University, and Zachary Lippman from CSHL.
Notably, some of these CNSs are remarkably ancient, with evidence indicating their existence predates the divergence of flowering plants from their non-flowering ancestors--dating back over 400 million years.
Innovative Genome Comparisons
How did the researchers unveil such a vast array of previously obscured regulatory sequences? The team meticulously examined the organization and composition of gene groups at a microscopic level. By analyzing the arrangement of these gene clusters across numerous plant genomes and tracing their lineage from ancestral species to modern varieties, they identified conserved elements that had eluded previous methods.
According to CSHL postdoc Anat Hendelman, a co-first author of the study, the team was astonished by the sheer number of unnoticed regulatory sequences. "Dissecting and genetically editing these CNSs confirmed their critical role in developmental functions," Hendelman explains.
Insights into Plant Regulatory DNA Evolution
The research also illuminated three key principles governing the evolution of CNSs in plant genomes. First, while the physical spacing between these sequences may vary, their order along chromosomes tends to remain stable. Second, during evolutionary rearrangements of plant genomes, CNSs can become associated with different genes. Finally, ancient CNSs often persist even after gene duplications, significantly influencing the evolution of plant genomes and gene families.
"This was one reason CNSs could not be discovered with the same methods used in animals," Lippman clarifies. "We not only identified CNSs through this innovative approach but also found that new regulatory sequences often evolve from modified ancient CNSs after gene duplication, shedding light on the emergence of novel regulatory elements."
A Comprehensive Resource for Plant Biology
The Conservatory initiative has created what researchers describe as a "comprehensive atlas of regulatory conservation across plants, including numerous crop species and their wild relatives." This valuable resource enables plant biologists, like CSHL collaborator David Jackson, to investigate how regulatory DNA has been preserved and transformed through plant evolution.
These findings hold significant implications for crop breeders facing challenges such as drought and food security. As Lippman asserts, "This discovery opens a new window into the evolution of life over eons and offers fresh opportunities to engineer or fine-tune crop traits more efficiently."