Chapter Three - Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range
Section snippets
Defining CRESS DNA Viruses
The term CRESS DNA viruses was coined in 2012 to refer to a group of single-stranded DNA (ssDNA) viruses encoding a replication-associated protein (Rep) that appears to be descended from a common ancestor. CRESS DNA stands for circular, Rep-encoding ssDNA and encompasses both prokaryotic and eukaryotic viruses, although the Reps of each of these groups have distinct characteristics (Koonin and Ilyina, 1993). Most ssDNA viruses are CRESS DNA viruses. Eleven out of thirteen ssDNA virus families
Discovery of Eukaryotic CRESS DNA Viruses
Although the first eukaryotic CRESS DNA viruses were only identified as such in the 1970s, symptoms consistent with CRESS DNA viral infection were described over a millennium ago. The common yellowing symptom of CRESS DNA viral infection of euphorbia leaves was the inspiration for a Japanese poet in 752 AD (Saunders et al., 2003), though the symptoms are not distinct enough for a definitive retrospective diagnosis. More definitively, plants with symptoms caused by geminiviruses were first
Unity and Diversity
While some eukaryotic CRESS DNA viruses have up to 10 open reading frames (ORFs), even the most compact genomes have two ORFs: one encoding the Rep and one encoding a capsid protein (CP). The conserved Rep serves as the anchor for this group of viruses, but the CP is highly divergent. Beyond the Rep and CP, protein content differs dramatically among CRESS DNA viruses.
Distribution and Sampling
We are not sure how close to the tip of the iceberg virologists are in terms of uncovering CRESS DNA viral diversity, but recent global efforts have more than doubled the number of eukaryotic CRESS DNA viral species in GenBank over the last 10 years (let alone the new strain sequences that add to our appreciation of the diversity within some eukaryotic CRESS DNA viral species). These abundant sequences come from a huge range of hosts and environments, and include both opportunistic sampling and
Eukaryotic CRESS DNA Viruses Evolve Quickly
Evolutionary study of eukaryotic CRESS DNA viruses is not restricted to paleovirology and untangling the deep phylogenetic relationships among families. Some eukaryotic CRESS DNA viruses are emergent pathogens, and the year-to-year evolution of these viruses impacts food security. For instance, novel begomoviruses have been a persistent emerging problem in crops including tomato (Ribeiro et al., 2003). Like emergent RNA viruses, eukaryotic CRESS DNA viruses have been shown to evolve quickly, a
Conclusions
Eukaryotic CRESS DNA viruses have been on the vanguard of the transition from detailed, molecular characterization of novel viruses to taxonomy by sequence similarity alone. Their small genome size, prevalence and affinity for rolling-circle replication allow easy molecular surveillance and high return on sampling effort. Virologists can now appreciate their incredible sequence diversity: varied genomic organization, divergence of the homologous Rep protein and novel viral proteins, which are
Acknowledgments
All authors acknowledge funding from the NSF Assembling the Tree of Life program (DEB-1239976 and DEB-1240049) and S.D. acknowledges funding from NSF OIA 1545553.
The nomenclature for this group of viruses has evolved over the last decade, and the authors would like to acknowledge the input of several ICTV members at the 2018 American Society for Virology meeting for the suggestions, including Poliane Alfenas-Zerbini, Mart Krupovic, Arvind Varsani and Murilo Zerbini.
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