Plant genomes contain more than just a record of ancient infections; they are a true molecular archive of evolution. An international research team led by scientists from INRAE and CIRAD discovered over 47,000 fragments of endogenous viruses from the Caulimoviridae family in the DNA of 93 plant species. These "molecular fossils" provide an unprecedented window into history spanning hundreds of millions of years, revealing viral evolution from the era when Earth's first vascular plants and ancient forests were just beginning to form.
Viruses of the Caulimoviridae family—the only known plant viruses with double-stranded DNA—possess a rare ability to integrate their genetic sequences into host chromosomes through non-localized recombination during DNA repair. These endogenous viral elements (EVEs), or "viral fossils," are passed down through generations and preserved for millions of years, turning the plant genome into a kind of diary recording the history of viral interactions. Researchers analyzed 93 plant species—ranging from mosses and clubmosses to ferns, conifers, and flowering plants—identifying 35 previously unknown evolutionary lineages of viruses, including a new cluster found only in certain coniferous tree species.
Comparing the evolutionary timelines of viruses and their plant hosts revealed a complex pattern of coexistence. Many viral lineages indeed existed alongside vascular plants for hundreds of millions of years, though their history was far from linear. Viruses jumped from one host species to another, while entire viral lineages vanished and reappeared. Several of these viral extinctions coincided with global planetary catastrophes—the Permian extinction (252 million years ago), which wiped out over 90% of marine species, and the Cretaceous-Paleogene extinction (66 million years ago) that killed the dinosaurs. During these periods, environmental conditions shifted drastically, restructuring ecosystems and creating new ecological niches.
These findings highlight how deeply viruses are woven into the fabric of life and evolution on Earth. Plant genomes serve not just as a reservoir of hereditary information, but as a genuine archive documenting hundreds of millions of years of interaction with invisible partners. Just as tree rings record the droughts and fires of past eras, viral sequences in DNA preserve the memory of moments when ecosystems experienced global upheaval and reshaped themselves in response.
The discovery prompts a rethink of the role viruses play in evolution: they do not just cause disease but appear to have helped shape the ability of plants to adapt to critical environmental changes. Even infections that caused damage in the distant past left traces in plant genes that today help us understand how living organisms cope with and recover from global crises.
The study, published in June 2026 in the journal PLoS Pathogens, opens a new path in paleovirology by using plant genomes as a natural archive of viral evolution. Scientists can now track how ancient viruses adapted to mass extinctions, climate change, and the emergence of new plant communities. This knowledge is critical for understanding modern interactions between plants and viral pathogens and may help predict how plants will respond to future environmental challenges.
Plant genomes are a living chronicle of millions of years of coexistence with viruses. The more closely we read this record, the better we understand how to protect the natural world from both present and future threats.
