Advances in sequencing technologies and bioinformatic analyses give rise to new research areas like ecogenomics, paleovirology, and phytobiome studies indicating that viruses are more abundant, and their roles in nature more diverse, than anticipated. Such modern sequencing technologies also facilitated the observation of partial or complete-genome DNA viruses within the host plant genomes revealing a myriad of endogenous viral elements (EVEs) in addition to already reported sequences of endogenous retroviruses (ERVs).

Our knowledge of plant viruses is affected by the available tools that can be used for their identification and characterization. Based on genome type and replication strategy, viruses with genome encoded by DNA form three groups according to Baltimore’s classification: single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and double-stranded with reverse transcription for replication activity (dsDNA-RT). In plants, identified DNA viruses were less common than RNA viruses, representing more or less 17% of plant viruses. Deep sequencing approaches have shown, thus far, that about half of the plant viruses classified by the International Committee on Taxonomy of Viruses (ICTV) carry a DNA genome, of which ssDNA being the most abundant genome type.

Unlike retroviruses, plant DNA viruses do not need to integrate into the host genome to replicate. This is likely the result of accidental illegitimate recombination occurring during the nucleus multiplication phase. When integration occurs in germinal cells, EVEs are systematically transmitted to the progenies and participate as ERVs to host genome evolution after endogenization, becoming in some cases viral fossil sequences. Besides being the cause of major diseases in crop plants, dsDNA-RT viruses can then participate in horizontal DNA transfer and can contribute to host genome evolution.

The mechanisms underlying these parasitic, mutual, or commensalism symbioses, involving active and fossil DNA viruses respectively with their plant hosts and invertebrate vectors, are complex.
The objective of the proposed issue aims to gather recent findings in this Research Topic field. Reviews and Original Research articles focused on these subtopics are welcome for submission:

• Co-evolution between the virus and viral gene with the host plant genome following endogenization
• Mechanism and impact of viral endogenization in evolution
• Contribution of DNA genomic fossils to plant genomes functions (gene function, gene expression, promoter, chromatin modifications, etc.) disease resistance and recovery.
• Interaction of EVEs with genomic TE (Metaviridae (Ty3/gypsy retrotransposons), Pseudoviridae (Ty1/copia retrotransposons), transposons)
• Host plant interactions (both positive and negative) with active and fossil dsDNA-RT viruses (innate, adaptive immunity)
• DNA virus-vector-plant interactions
• DNA virus interactions with the phytobiome
• Mechanisms underlying symptom expression, latency of plant DNA viruses
• Bioinformatic tools to study DNA virus evolution, epidemiology, and taxonomy.

Studies that only describe new viral genome sequences accompanied with basic phylogenetic analyses will not be considered for review unless they are extended to provide novel and meaningful insights into gene/protein function and/or the biology of the virus.

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Frontiers in Plant Science

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