Recombination in Eukaryotic Single Stranded DNA Viruses

Abstract

Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

“…Recombination is known to have an important role in the evolution of eukaryotic ssDNA viruses 13,19 . However, interfamilial gene exchange has not been convincingly demonstrated for these viruses, suggesting that such recombination might be either uncommon or the recombinants are rarely retained in the population.…”

“…A characteristic feature of RC-Reps of eukaryotic ssDNA viruses is the presence of the superfamily 3 helicase (S3H) domain 16,17 , which is fused carboxy-terminally to the catalytic nuclease domain encompassing three signature motifs found in all prokaryotic and eukaryotic virus and plasmid RC-Reps 14 . As opposed to CPs, RC-Reps of eukaryotic viruses display actual sequence similarity and RC-Rep-based phylogenies recapitulate the major taxonomic groups defined by the International Committee on Taxonomy of Viruses 1,18,19 . However, it should be noted that not all eukaryotic ssDNA viruses possess genes for canonical RC-Reps; for example, anelloviruses-even though believed to replicate via RC mechanism-do not encode a protein that would contain the entire set of motifs characteristic to RC-Reps 17 .…”

“…Alternatively, similarity between the RC-Reps of ssDNA viruses and prokaryotic plasmids on the one hand 14,15,21,22 and structural similarity between the CPs of viruses with ssDNA and ssRNA genomes on the other 13 led to the proposal that different groups of ssDNA viruses have emerged from plasmids by acquisition of CP-coding genes from RNA viruses, possibly on multiple independent occasions 12,13,23 . Indeed, both homologous and illegitimate recombination have important roles in driving the evolution of ssDNA viruses 19 .…”

Potential role of viruses in white plague coral disease

“…The Rep initiator protein was selected as a marker because of its evolutionary conservation in all SCSDVs and their associated satellite DNAs (Ilyina and Koonin, 1992;Gibbs and Weiller, 1999;Martin et al, 2011;Delwart and Li, 2012). METAVIR conducts the following steps to construct phylogenetic comparisons:…”

Construction of an Infectious Chimeric Geminivirus by Molecular Cloning Based on Coinfection and Recombination

“…Major factors including the whitefly biotypes dominance, emergence and recombination of viruses by expanding their host range and the betasatellite ability to interact with manifold begomoviruses contribute significantly to the emergence and resurgence of geminiviruses (Seal et al, 2006). In monocot and dicot infecting mastreviruses, very similar ecological, evolutionary and biochemical factors trigger recombination patterns irrespective of the differences in host range (Martin et al, 2011). Acquisition of recombination in some mastreviruses leading to the establishment of some novel traits that prompt the emergence of pathogens (Varsani et al, 2008).…”