Plant DNA Harbours Virus ‘Fossils' That Reflect 300 Million Years of Evolution

An international team of INRAE and CIRAD researchers answered an intriguing question by exploring plant genomes to find the molecular fossils of viruses. During infections, genome fragments from certain viruses can become embedded in their hosts' chromosomes. These endogenous viral elements can be transmitted across generations for millions of years, serving as evolutionary records of virus infections in plants. The research team focused on the plant virus family Caulimoviridae , which is known for becoming embedded in host genomes as evolutionarily persistent endogenous elements. The researchers analysed the genomes of 93 representative species from all the major lineages of terrestrial plants, including mosses, lycophytes, ferns, conifers, and flowering plants. They identified more than 47,000 endogenous viral elements left by members of Caulimoviridae . The findings show that Caulimoviridae viruses have infected an extremely wide range of vascular plant hosts, from lycophytes to flowering plants. The researchers also discovered that virus diversity within this family has been greatly underestimated. Their work revealed the existence of 35 previously undescribed taxonomic clusters in Caulimoviridae , including a newly described clade found only in certain conifers. When the researchers compared the evolutionary history of Caulimoviridae viruses to that of their plant hosts, they found that several virus taxonomic clusters appeared to have 'co-evolved with vascular plants for several hundred million years.' However, this relationship was not always linear. Instead, their shared history was complex: sometimes viruses switched hosts, and sometimes they went extinct. Several extinction events may have been tied to mass extinction events during the late Permian (252 million years ago) and the late Cretaceous (66 million years ago). These events reshaped terrestrial ecosystems, leading to species disappearance and the creation of new ecological niches. This work has underscored the great value of plant genomes as 'natural records of virus evolution.' Researchers can utilise the traces left behind by ancient infections to illuminate the enduring interactions between plants and their viruses and the ways viruses mechanistically adapt to ecosystem shifts. Journal: PLOS Pathogens DOI: 10.1371/journal.ppat.1014340 Article Title: Endogenous viral elements trace the ancient origins and early evolution of the Caulimoviridae Publication Date: June 26, 2026 Featured image credit: Madison Inouye/Pexels Source: EurekAlert