Discovery, Prevalence, and Persistence of Novel Circular Single-Stranded DNA Viruses in the Ctenophores Mnemiopsis leidyi and Beroe ovata

Discovery of Four Novel Circular Single-Stranded DNA Viruses in Fungus-Farming Termites

Genome Announcements ◽

10.1128/genomea.00318-18 ◽

2018 ◽

Vol 6 (17) ◽

Cited By ~ 5

Author(s):

Mason Kerr ◽

Karyna Rosario ◽

Christopher C. M. Baker ◽

Mya Breitbart

Keyword(s):

Termite Mounds ◽

Single Stranded Dna ◽

Dna Viruses ◽

Content Type ◽

The Family

ABSTRACT Here, we describe four novel circular single-stranded DNA viruses discovered in fungus-farming termites ( Odontotermes sp.). The viruses, named termite-associated circular virus 1 (TaCV-1) through TaCV-4, are most similar to members of the family Genomoviridae and were widely detected in African termite mounds.

Download Full-text

Peer Review #2 of "Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils (v0.1)"

10.7287/peerj.7265v0.1/reviews/2 ◽

2019 ◽

Author(s):

C Bellas

Keyword(s):

Peer Review ◽

Single Stranded Dna ◽

Dna Viruses

Download Full-text

An improved experimental pipeline for preparing circular ssDNA viruses for next-generation sequencing

10.1101/2020.09.30.321224 ◽

2020 ◽

Cited By ~ 1

Author(s):

Catherine D. Aimone ◽

J. Steen Hoyer ◽

Anna E. Dye ◽

David O. Deppong ◽

Siobain Duffy ◽

...

Keyword(s):

Next Generation Sequencing ◽

Rolling Circle Amplification ◽

Next Generation ◽

Viral Dna ◽

Single Stranded Dna ◽

Dna Viruses ◽

Short Read ◽

Rolling Circle ◽

Optimized Protocol ◽

Generation Sequencing

AbstractWe present an optimized protocol for enhanced amplification and enrichment of viral DNA for Next Generation Sequencing of begomovirus genomes. The rapid ability of these viruses to evolve threatens many crops and underscores the importance of using next generation sequencing efficiently to detect and understand the diversity of these viruses. We combined enhanced rolling circle amplification (RCA) with EquiPhi29 polymerase and size selection to generate a cost-effective, short-read sequencing method. This optimized protocol produced short-read sequencing with at least 50% of the reads mapping to the viral reference genome. We provide other insights into common misconceptions about RCA and lessons we have learned from sequencing single-stranded DNA viruses. Our protocol can be used to examine viral DNA as it moves through the entire pathosystem from host to vector, providing valuable information for viral DNA population studies, and would likely work well with other CRESS DNA viruses.HighlightsProtocol for short-read, high throughput sequencing of single-stranded DNA viruses using random primersComparison of the sequencing of total DNA versus size-selected DNAComparison of phi29 and Equiphi29 DNA polymerases for rolling circle amplification of viral single-stranded DNA genomes

Download Full-text

Peer Review #2 of "Towards quantitative viromics for both double-stranded and single-stranded DNA viruses (v0.1)"

10.7287/peerj.2777v0.1/reviews/2 ◽

2016 ◽

Keyword(s):

Peer Review ◽

Single Stranded Dna ◽

Dna Viruses

Download Full-text

Pervasive Chimerism in the Replication-Associated Proteins of Uncultured Single-Stranded DNA Viruses

Viruses ◽

10.3390/v10040187 ◽

2018 ◽

Vol 10 (4) ◽

pp. 187 ◽

Cited By ~ 27

Author(s):

Darius Kazlauskas ◽

Arvind Varsani ◽

Mart Krupovic

Keyword(s):

Single Stranded Dna ◽

Dna Viruses ◽

Associated Proteins

Download Full-text

Novel circular DNA virus identified in Opuntia discolor (Cactaceae) that codes for proteins with similarity to those of geminiviruses

Journal of General Virology ◽

10.1099/jgv.0.001671 ◽

2021 ◽

Vol 102 (11) ◽

Author(s):

Rafaela S. Fontenele ◽

Matias Köhler ◽

Lucas C. Majure ◽

Jesús A. Avalos-Calleros ◽

Gerardo R. Argüello-Astorga ◽

...

Keyword(s):

South America ◽

Rolling Circle Replication ◽

Dna Virus ◽

Single Stranded Dna ◽

Dna Viruses ◽

Circular Dna ◽

Rolling Circle ◽

Rep Protein ◽

Molecular Features ◽

Viral Components

Viral metagenomic studies have enabled the discovery of many unknown viruses and revealed that viral communities are much more diverse and ubiquitous than previously thought. Some viruses have multiple genome components that are encapsidated either in separate virions (multipartite viruses) or in the same virion (segmented viruses). In this study, we identify what is possibly a novel bipartite plant-associated circular single-stranded DNA virus in a wild prickly pear cactus, Opuntia discolor, that is endemic to the Chaco ecoregion in South America. Two ~1.8 kb virus-like circular DNA components were recovered, one encoding a replication-associated protein (Rep) and the other a capsid protein (CP). Both of the inferred protein sequences of the Rep and CP are homologous to those encoded by members of the family Geminiviridae. These two putatively cognate components each have a nonanucleotide sequence within a likely hairpin structure that is homologous to the origins of rolling-circle replication (RCR), found in diverse circular single-stranded DNA viruses. In addition, the two components share similar putative replication-associated iterative sequences (iterons), which in circular single-stranded DNA viruses are important for Rep binding during the initiation of RCR. Such molecular features provide support for the possible bipartite nature of this virus, which we named utkilio virus (common name of the Opuntia discolor in South America) components A and B. In the infectivity assays conducted in Nicotiana benthamiana plants, only the A component of utkilio virus, which encodes the Rep protein, was found to move and replicate systemically in N. benthamiana. This was not true for component B, for which we did not detect replication, which may have been due to this being a defective molecule or because of the model plants (N. benthamiana) used for the infection assays. Future experiments need to be conducted with other plants, including O. discolor, to understand more about the biology of these viral components.

Download Full-text

Single-Stranded DNA Viruses in Antarctic Cryoconite Holes

Viruses ◽

10.3390/v11111022 ◽

2019 ◽

Vol 11 (11) ◽

pp. 1022 ◽

Cited By ~ 5

Author(s):

Pacifica Sommers ◽

Rafaela S. Fontenele ◽

Tayele Kringen ◽

Simona Kraberger ◽

Dorota L. Porazinska ◽

...

Keyword(s):

Microbial Communities ◽

Open Reading Frames ◽

Pairwise Identity ◽

Capsid Protein Gene ◽

Single Stranded Dna ◽

Dna Viruses ◽

Viral Genomes ◽

Freshwater Pond ◽

Dry Valley ◽

Population Structures

Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.

Download Full-text