While the extent and importance of endogenous viral elements have been thoroughly researched in animals, there is a dearth of knowledge when it comes to plants. Within the framework of a broader international effort, researchers at INRA Versailles-Grignon and Cirad have described a new genus of the Caulimoviridae family of viruses, called Florendovirus, whose members have colonised the genomes of a wide range of flowering plants throughout the course of evolution. Their findings are published in the November 10, 2014 issue of the journal Nature Communications.
Viruses of the Caulimoviridae family are at the root of many plant infections. Like all of their kind, they are strictly intracellular parasites, meaning they must interact very closely with their host in order to develop. While scientists have good knowledge of the insertion of viral elements in animal genomes, this is not the case with plants. As part of an international collaboration, researchers at INRA and Cirad have delved into this issue, making important strides.
New viral sequences in genomes of flowering plants
Thanks to scientific knowledge and genomic and bio-informatic tools, researchers have been able to identify hitherto unknown elements of viral sequences in the grapevine genome (Vitis vinifera). The assembly of these endogenous sequences enabled them to reconstruct a viral genome with a genetic composition close to that of Caulimoviridae.
Researchers then went on to analyse the genome of 31 plants representing the different phylogenetic groups characterised to date, from green algae to flowering plants. They found a high proportion of these endogenous viral sequences of a new genus (between 0.5% and 1% of the genome) in 21 flowering plants, while they were absent in the genomes of more primitive plants such as moss, green algae or selaginella (spikemoss). Targeted analysis of the genomes of the plants in question led to the assembly of76 viral genomes related to Caulimoviridae.
According to research, these sequences may have come about as a result of physical contact between flowering plants and viruses of a new phylogenetic group within the Caulimoviridae family. These viruses have been dubbed "Florendovirus", a composite of Flora, the name of the Roman goddess of flowers, and the adjective endogenous. The different species of Florendovirus are differentiated by the name of their host plant; for example, "Vitis vinifera virus", or "VvinV".
Insertions over the course of evolution
Because scientists have access to the genomes of several varieties of rice (Oryza spp.) and know the history of their evolution, they are able to date the invasion of Florendovirus in plant genomes to over 1.8 million years ago. More broadly, they can place the endogenisation process of Florendovirus into the bigger evolutionary picture of flowering plants. A second approach, based on phylogeographic evidence - that is, evidence related to the distribution and geographical structuring of populations - would suggest that Florendovirus goes back much further, to between 20 and 30 million years ago.
Functions still to be determined
The vast majority of reconstructed Florendovirus genomes have two open reading frames, or ORFs*. The first encodes a significant protein believed to be involved in the movement or establishment of the viral capsid; the second encodes a protein specific to this new viral genus whose function is still unknown. Some of these genomes have a unique bipartite organisation, such as two circular DNA that carry complimentary information, the significance of which has yet to be determined.
These findings and the description of a new genus of virus constitute a significant scientific breakthrough, boosting knowledge of plants, and notably plants of agricultural interest and the pathogens that affect them. These are major strides in the emerging field of paleovirology.
Science may well have much more to learn from Florendovirus. Its high frequency in plant genomes seems to suggest a major role in the evolution of plant genomes, whether through the provision of new genetic material or regulating gene expression.
* A reading frame is a sequence of codons that constitute genetic information translated into proteins. Each codon is made up of three nucleotides, and reading can start with any of the three. There are therefore three possible reading frames per DNA strand.
Reference
Andrew D. W. Geering, Florian Maumus, Dario Copetti, Nathalie Choisne, Derrick J. Zwickl, Matthias Zytnicki, Alistair R. McTaggart, Simone Scalabrin, Silvia Vezzulli, Hadi Quesneville, Pierre-Yves Teycheney. Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nature Communications, 10 November 2014. DOI: 10.1038/ncomms6269