Unveiling Crucivirus Diversity by Mining Metagenomic Data

Abstract

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses. IMPORTANCE Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.

Genetic diversity and characterization of circular replication(Rep)-encoding single-stranded (CRESS) DNA viruses

“…Recently, it has been reported that the cap protein of Cruciviruses is very similar, but the Rep protein may be derived from different sources with greater diversity 17 ; we examined whether the sequences in the cluster of these 20 Cap proteins received the Rep protein from the same group or from different groups. To do this, we took the representative sequences in each Cap-cluster and identified the phylogenetic tree groups that contain its Rep protein ( Supplementary Data 19 ).…”

“…This is because Rep protein contains conserved HUH motif, and S3H domains, while Cap protein is unclassified because it has high genetic diversity without being conserved 1,12 . However, of the cruciviruses that classify Cap protein well, the report that Cap proteins are nearly identical and that the highly diverse Rep protein may be derived from different CRESS-DNA virus sources is critical here 17 .…”

New World Cactaceae Plants Harbor Diverse Geminiviruses

“…Hence, we undertook a sequence similarity network analysis of the CP amino acid sequences of all geminiviruses (with a >90% identity cut off) and further associated the identified clusters with the known insect vectors (Figure 8). Sequence similarity network analyses are useful for clustering groups of similar protein sequences in large datasets relatively quickly (see [48,[106][107][108] for examples). Unlike OpV1, which forms its own distinct cluster [15], indicating that it is likely transmitted by an insect vector that has not yet been associated with geminiviruses, OpV2 CPs cluster with those of curtoviruses, becurtoviruses (including Opuntia becurtovirus), and two unclassified viruses (parsley yellow leaf curl virus and Limeum africanum-associated virus).…”

“…Nonetheless, our viral load analysis suggests that the viral load of Opuntia becurtovirus in cactus samples and experimentally inoculated N. benthamiana plants is low compared to those of OpV1 and OpV2. [48, [106][107][108] for examples). Unlike OpV1, which forms its own distinct cluster [15], indicating that it is likely transmitted by an insect vector that has not yet been associated with geminiviruses, OpV2 CPs cluster with those of curtoviruses, becurtoviruses (including Opuntia becurtovirus), and two unclassified viruses (parsley yellow leaf curl virus and Limeum africanum-associated virus).…”

Identification and Distribution of Novel Cressdnaviruses and Circular Molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula

“…In general, for viruses in the phylum Cressdnaviricota, the CPs are more diverse than the Reps. Furthermore, the CPs of geminiviruses share homology to those of albetoviruses (linear ssRNA(+) genomes) [65], and a group of unclassified cressdnavirues have CPs that are homologous to those of tombusviruses (linear ssRNA(+) genomes) [64,[66][67][68].…”