Circular, Rep-encoding single-stranded (CRESS) DNA viruses were once thought to be a rare kind of viral genomic architecture. While some significant agricultural diseases were caused by circoviruses and geminiviruses, they are not typically human pathogens, and it was only when metagenomic methods that were not biased towards double-stranded DNA were widely used did we identify single-stranded DNA viruses ubiquitously. Many of these sequence-only identified genomes don’t look like the characterized genera that scientists can grow in the lab, but the one commonality among most of these genomes is that they have a recognizable Replication-associated protein (Rep) that is homologous with all other eukaryote-infecting CRESS DNA viruses. As we attempt to understand the evolution of this large and speciose group, we have identified idiosyncratic patterns in their nucleotide use, their protein evolution and have created a Rep genealogy that represents the evolution of their shared ORF. Recently systematized groups of CRESS DNA viruses have not plumbed the depths of the uncharacterized viral diversity that has been sequenced, and the Rep tree suggests that existing families of CRESS DNA viruses may not be independently evolving — we suggest there is a common origin of the intron in the Rep of some geminiviriuses and all gemonoviruses. CRESS DNA viruses are a newly discovered component of microbiomes across eukaryotes and in environmental samples, and we are starting to understand how these pathogens have diversified over evolutionary time.
1. Appreciate the ecological and molecular diversity of CRESS DNA viruses that infect eukaryotes.
2. Understand how the molecular evolution of unique groups of viruses differ from one another, and the value of accurate model choice in phylogenetics.