A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics

Rosario, Karyna; Duffy, Siobain; Breitbart, Mya

doi:10.1007/s00705-012-1391-y

Cited by 284 publications

(396 citation statements)

References 115 publications

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“…In circoviruses, the loop contains a conserved motif of 9 bp (i.e. nonanucleotide) located between the 5 0 -ends of the two main inversely encoded open-reading frames (King et al, 2012;Rosario et al, 2012). Phylogenetic analysis of the replication protein sequences revealed at least 10 new clades of environmental ssDNA viruses that are distinct from terrestrial viruses ( Figure 5 and Supplementary Figure 4).…”

Section: Resultsmentioning

confidence: 99%

“…Sequences with similarity to ssDNA viruses have been found in metagenomic data from multiple environments (reviewed in Rosario and Breitbart, 2011;Rosario et al, 2012). For example, sequences from the Microviridae and Circoviridae have been observed in marine environments (Angly et al, 2006;Rosario et al, 2009), freshwater (Ló pez-Bueno et al, 2009) and modern stromatolites , and similar to those from the Circoviridae, Geminiviridae, Nanoviridae and Parvoviridae were observed in corals (Thurber et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Previously unknown and highly divergent ssDNA viruses populate the oceans

2013

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Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Previously unknown and highly divergent ssDNA viruses populate the oceans

2013

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“…Active infection of Symbiodinium by members of the Phycodnaviridae was indirectly demonstrated based on the identification of phycodnavirus-like complementary DNAs in cultures of two different clades of Symbiodinium . Finally, sequence similarities to and viral-like particles reminiscent of nano-, circo-and geminiviruses, all of which are eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses and their associated satellites (collectively referred to 'SCSDVs' in this paper) also have been found in corals (Davy and Patten, 2007;Wegley et al, 2007;Marhaver et al, 2008;Patten et al, 2008;Vega Thurber et al, 2008;Littman et al, 2011;Rosario et al, 2012).…”

Section: Introductionmentioning

confidence: 81%

“…SCSDVs are common pathogens of plants and animals and include the families: Circoviridae, Nanoviridae, Geminiviridae, but their prevalence and distribution in the environment was unknown until recently. Based on metagenomic analyses of animal hosts (for example, human, bat, rodent, pig and chimpanzee) and water samples, SCSDVs are now thought to be more common than previously thought (for review, Rosario et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

“…The host for the coral-associated SCSDVs presented here is yet to be determined, but may include the algal endosymbiont (Symbiodinium spp., because nanovirus/geminiviruses infect plants), the coral host itself (because circoviruses infect animals), or another member of the coral holobiont (Yu et al, 2010;Delwart and Li, 2012;Rosario et al, 2012;). However, a previous study examining viruses associated with Montastraea cavernosa coral colonies searched Symbiodinium EST libraries and found few similarities to SCSDVs suggesting that the SCSDVs associated with diseased corals in this study are infecting the coral animal.…”

Section: Discussionmentioning

confidence: 99%

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Potential role of viruses in white plague coral disease

Soffer

Brandt

Correa³

et al. 2013

The ISME Journal

108

121

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White plague (WP)-like diseases of tropical corals are implicated in reef decline worldwide, although their etiological cause is generally unknown. Studies thus far have focused on bacterial or eukaryotic pathogens as the source of these diseases; no studies have examined the role of viruses. Using a combination of transmission electron microscopy (TEM) and 454 pyrosequencing, we compared 24 viral metagenomes generated from Montastraea annularis corals showing signs of WP-like disease and/or bleaching, control conspecific corals, and adjacent seawater. TEM was used for visual inspection of diseased coral tissue. No bacteria were visually identified within diseased coral tissues, but viral particles and sequence similarities to eukaryotic circular Rep-encoding single-stranded DNA viruses and their associated satellites (SCSDVs) were abundant in WP diseased tissues. In contrast, sequence similarities to SCSDVs were not found in any healthy coral tissues, suggesting SCSDVs might have a role in WP disease. Furthermore, Herpesviridae gene signatures dominated healthy tissues, corroborating reports that herpes-like viruses infect all corals. Nucleocytoplasmic large DNA virus (NCLDV) sequences, similar to those recently identified in cultures of Symbiodinium (the algal symbionts of corals), were most common in bleached corals. This finding further implicates that these NCLDV viruses may have a role in bleaching, as suggested in previous studies. This study determined that a specific group of viruses is associated with diseased Caribbean corals and highlights the potential for viral disease in regional coral reef decline.

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Circular Nucleic Acids: Discovery, Functions and Applications

Mohammed-Elsabagh

Paczkowski

et al. 2020

ChemBioChem

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acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topologycontrolled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.[a] Dr.

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A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics

Cited by 284 publications

References 115 publications

Previously unknown and highly divergent ssDNA viruses populate the oceans

Previously unknown and highly divergent ssDNA viruses populate the oceans

Potential role of viruses in white plague coral disease

Circular Nucleic Acids: Discovery, Functions and Applications

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