Biology subjects

Teycheney, P.-Y.

Publications and source records attributed to Teycheney, P.-Y..

2 recordsLinked to original sources

bioRxiv2025

The diversity and host range of endogenous caulimovirids illuminate the ancient origin and early evolution of the Caulimoviridae

Endogenous viral elements (EVEs) are viral sequences integrated into the genomes of host organisms, analogous to molecular fossils. The majority of characterised EVEs in plants are derived from the Caulimoviridae, the only family of dsDNA viruses infecting this kingdom. Endogenous caulimovirids (ECVs) occur across taxonomically diverse vascular plant species and represent a significant resource for studying host-virus coevolution, host range dynamics, and the evolution of viral genomes over deep timescales. Previous evolutionary studies based on ECVs proposed either cospeciation or host-switching as the main drivers of Caulimoviridae evolution, but were limited by sparse genomic data from basal plant lineages. Using 93 plant genomes spanning all embryophyte lineages, including ferns and lycophytes, we identified 47,135 ECVs in 75 genomes. These were grouped into 71 operational taxonomic units (OTUs), including 35 novel ones, revealing unexpected Caulimoviridae diversity in vascular plants and a new clade restricted to gymnosperms. Phylogenetic comparisons with host plant taxonomy support a macroevolutionary scenario in which cospeciation with tracheophytes drove the diversification of Caulimoviridae. Our findings position Caulimoviridae and ECVs as a reference system for paleovirology, offering unprecedented insights into how plant viruses and their hosts coevolved, diversified, and sometimes went extinct.

evolutionary biology↗

bioRxiv2017

Tracheophyte genomes keep track of the deep evolution of the Caulimoviridae

Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of their hosts and are signatures of viral infections that may have occurred millions of years ago. The study of EVEs, coined paleovirology, provides important insights into virus evolution. The Caulimoviridae is the most common group of EVEs in plants, although their presence has often been overlooked in plant genome studies. We have refined methods for the identification of caulimovirid EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced flowering plants. Evidence is provided that almost every vascular plant (tracheophyte), including the most primitive taxa (clubmosses, ferns and gymnosperms) contains caulimovirid EVEs, many of which represent previously unrecognized evolutionary branches. In angiosperms, EVEs from at least one and as many as five different caulimovirid genera were frequently detected, and florendoviruses were the most widely distributed, followed by petuviruses. From the analysis of the distribution of different caulimovirid genera within different plant species, we propose a working evolutionary scenario in which this family of viruses emerged at latest during Devonian era (approx. 320 million years ago) followed by vertical transmission and by several cross-division host swaps.

evolutionary biology↗