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Arvind Varsani - One of the best experts on this subject based on the ideXlab platform.
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Identification of circular single-stranded DNA Viruses in faecal samples of Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus) inhabiting the Colorado San Juan Mountains
Infection Genetics and Evolution, 2018Co-Authors: Simona Kraberger, Kara Waits, Jake Ivan, Eric S. Newkirk, Sue Vandewoude, Arvind VarsaniAbstract:Abstract The San Juan Mountains of southern Colorado provide subalpine habitat for a suite of mammalian species including Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus). In the winter field season of 2016 five faecal samples from lynx, and one each from moose and snowshoe hare were collected to identify small single-stranded DNA Viruses associated with these three prominent species. Thirty-two novel Viruses were identified and classified as members of two well established ssDNA families Genomoviridae (n = 22) and Microviridae (n = 10) and one recently proposed new family, Smacoviridae (n = 1). In addition one highly novel circular ssDNA virus was identified which at present does not group with any known family. A high level of genomovirus diversity was identified from faeces collected between and across the three mammal species, with full genome-wide pairwise comparisons showing 57%–97% identity. Twenty genomoViruses can be assigned to the genus Gemycircularvirus and represent 11 species, and two into a distinct species in the genus Gemykolovirus. The single smacovirus identified from moose also represents a distinct smacovirus species. Ten microViruses, seven from moose, one from snowshoe hare and two from lynx, all are part of the Gokushovirinae subfamily. The two from lynx are highly similar to a microvirus previously detected in domestic cat (sharing 88%–90% genome-wide identity), indicating this may be a common felid gut microbiome associated virus. Our findings highlight the broad range of diverse ssDNA Viruses present in three mammals inhabiting the San Juan Mountains.
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Identification of novel Bromus- and Trifolium-associated circular DNA Viruses
Archives of Virology, 2015Co-Authors: Simona Kraberger, Darren P. Martin, Gerardo R. Argüello-astorga, Kata Farkas, Pauline Bernardo, Cameron Booker, François Mesléard, Philippe Roumagnac, Arvind VarsaniAbstract:The genomes of a large number of highly diverse novel circular DNA Viruses from a wide range of sources have been characterised in recent years, including circular single-stranded DNA (ssDNA) Viruses that share similarities with plant-infecting ssDNA Viruses of the family Geminiviridae . Here, we describe six novel circular DNA viral genomes that encode replication-associated (Rep) proteins that are most closely related to those of either geminiViruses or gemycircularViruses (a new group of ssDNA Viruses that are closely related to geminiViruses). Four possible viral genomes were recovered from Bromus hordeaceus sampled in New Zealand, and two were recovered from B. hordeaceus and Trifolium resupinatum sampled in France. Two of the viral genomes from New Zealand (one from the North Island and one from the South Island each) share >99 % sequence identity, and two genomes recovered from B. hordeaceus and T. resupinatum sampled in France share 74 % identity. All of the viral genomes that were recovered were found to have a major open reading frame on both their complementary and virion-sense strands, one of which likely encodes a Rep and the other a capsid protein. Although future infectivity studies are needed to identify the host range of these Viruses, this is the first report of circular DNA Viruses associated with grasses in New Zealand.
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Diverse small circular single-stranded DNA Viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica)
Infection Genetics and Evolution, 2014Co-Authors: Peyman Zawar-reza, Simona Kraberger, Gerardo R. Argüello-astorga, Daisy Stainton, Laurel Julian, Paul A. Broady, Arvind VarsaniAbstract:Abstract Antarctica has some of the harshest environmental conditions for existence of life on Earth. In this pilot study we recovered eight diverse circular single-stranded DNA (ssDNA) viral genome sequences (1904–3120 nts) from benthic mats dominated by filamentous cyanobacteria in a freshwater pond on the McMurdo Ice Shelf sampled in 1988. All genomes contain two to three major open reading frames (ORFs) that are uni- or bi-directionally transcribed and all have an ORF encoding a replication-associated protein (Rep). In one genome, the second ORF has similarity to a capsid protein (CP) of Nepavirus which is most closely related to geminiViruses. Additionally, all genomes have two intergenic regions that contain putative stem loop structures, six genomes have NANTATTAC as the nonanucleotide motif, while one has CCTTATTAC, and another has a non-canonical stem loop. In the large intergenic region, we identified iterative sequences flanking the putative stem-loop elements which are a hallmark of most circular ssDNA Viruses encoding rolling circle replication (RCR) initiators of the HUH endonuclease superfamily. The Reps encoded by ssDNA viral genomes recovered in this study shared
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novel circular dna Viruses identified in procordulia grayi and xanthocnemis zealandica larvae using metagenomic approaches
Infection Genetics and Evolution, 2014Co-Authors: Anisha Dayaram, Mark L Galatowitsch, Jon S Harding, Gerardo R Arguelloastorga, Arvind VarsaniAbstract:Recent advances in sequencing and metagenomics have enabled the discovery of many novel single stranded DNA (ssDNA) Viruses from various environments. We have previously demonstrated that adult dragonflies, as predatory insects, are useful indicators of ssDNA Viruses in terrestrial ecosystems. Here we recover and characterise 13 viral genomes which represent 10 novel and diverse circular replication associated protein (Rep)-encoding single stranded (CRESS) DNA Viruses (1628–2668 nt) from Procordulia grayi and Xanthocnemis zealandica dragonfly larvae collected from four high-country lakes in the South Island of New Zealand. The dragonfly larvae associated CRESS DNA Viruses have different genome architectures, however, they all encode two major open reading frames (ORFs) which either have bidirectional or unidirectional arrangement. The 13 viral genomes have a conserved NAGTATTAC nonanucleotide motif and in their predicted Rep proteins we identified the rolling circle replication (RCR) motif 1, 2 and 3, as well as superfamily 3 (SF3) helicase motifs. Maximum likelihood phylogenetic and pairwise identity analysis of the Rep amino acid sequences reveal that the dragonfly larvae novel CRESS DNA Viruses share <63% pairwise amino acid identity to the Reps of other CRESS DNA Viruses whose complete genomes have been determined and available in public databases and that these Viruses are novel. CRESS DNA Viruses are circulating in larval dragonfly populations; however, we are unable to ascertain whether these Viruses are infecting the larvae directly or are transient within dragonflies via their diet.
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novel myco like dna Viruses discovered in the faecal matter of various animals
Virus Research, 2013Co-Authors: Alyssa Sikorski, Darren P. Martin, Arvind Varsani, Simona Kraberger, Melanie Massaro, Laura M Young, Darren SmalleyAbstract:Abstract A wide variety of novel single-stranded DNA (ssDNA) Viruses have been found in faecal matter of chimpanzees, cows, rodents, bats, badgers, foxes and pigs over the last few years. Using a combination of rolling circle amplification coupled with restriction enzyme digests based approach as well as a next generation sequencing informed approach, we have recovered fourteen full genomes of ssDNA Viruses which exhibit genomic features described for members of the recently proposed gemycircularvirus group from a wide variety of mammal and bird faecal samples across New Zealand. The fourteen novel ssDNA Viruses (2122–2290 nt) encode two major proteins, a replication associated protein (Rep) and a capsid protein (Cp) which are bi-directionally transcribed. Interestingly, the Rep of these novel Viruses are similar to gemycircularViruses detected in insects, cassava leaves, and badger faecal matter, the novel Viruses share sequence similarities with the mycovirus sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) and Rep-like sequences found in fungal genomes. Pairwise sequence similarities between the 14 novel genomes with other related viral isolates (gemycircularViruses) indicated that they share greater than 55.8% genome-wide identity. Additionally, they share between 55% and 59% pairwise identity with putative novel ssDNA virus genomes recently isolated from sewage baminivirus, niminivirus and nephavirus. Based on the similarities to SsHADV-1 and Rep-like sequences found in fungal genomes, these novel gemycircularViruses may infect fungi.
Edward C Holmes - One of the best experts on this subject based on the ideXlab platform.
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phylogenetic evidence for rapid rates of molecular evolution in the single stranded dna begomovirus tomato yellow leaf curl virus
Journal of Virology, 2008Co-Authors: Siobain Duffy, Edward C HolmesAbstract:for protein-coding regions. The intergenic region, which is known to be more variable, was found to evolve even more rapidly, with a mean substitution rate of 1.56 10 3 subs/site/year. Notably, these substitution rates, the first reported for a plant DNA virus, are in line with those estimated previously for mammalian ssDNA Viruses and RNA Viruses. Our results therefore suggest that the high evolutionary rate of the geminiViruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts.
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phylogenetic evidence for rapid rates of molecular evolution in the single stranded dna begomovirus tomato yellow leaf curl virus
Journal of Virology, 2008Co-Authors: Siobain Duffy, Edward C HolmesAbstract:GeminiViruses are devastating Viruses of plants that possess single-stranded DNA (ssDNA) DNA genomes. Despite the importance of this class of phytopathogen, there have been no estimates of the rate of nucleotide substitution in the geminiViruses. We report here the evolutionary rate of the tomato yellow leaf curl disease-causing Viruses, an intensively studied group of monopartite begomoViruses. Sequences from GenBank, isolated from diseased plants between 1988 and 2006, were analyzed using Bayesian coalescent methods. The mean genomic substitution rate was estimated to be 2.88 x 10(-4) nucleotide substitutions per site per year (subs/site/year), although this rate could be confounded by frequent recombination within Tomato yellow leaf curl virus genomes. A recombinant-free data set comprising the coat protein (V1) gene in isolation yielded a similar mean rate (4.63 x 10(-4) subs/site/year), validating the order of magnitude of genomic substitution rate for protein-coding regions. The intergenic region, which is known to be more variable, was found to evolve even more rapidly, with a mean substitution rate of approximately 1.56 x 10(-3) subs/site/year. Notably, these substitution rates, the first reported for a plant DNA virus, are in line with those estimated previously for mammalian ssDNA Viruses and RNA Viruses. Our results therefore suggest that the high evolutionary rate of the geminiViruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts.
Siobain Duffy - One of the best experts on this subject based on the ideXlab platform.
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A comprehensive genealogy of the replication associated protein of CRESS DNA Viruses reveals a single origin of intron-containing Rep
2019Co-Authors: Lele Zhao, Erik Lavington, Siobain DuffyAbstract:Abstract Abundant novel circular Rep-encoding ssDNA Viruses (CRESS DNA Viruses) have been discovered in the past decade, prompting a new appreciation for the ubiquity and genomic diversity of this group of Viruses. Although highly divergent in the hosts they infect or are associated with, CRESS DNA Viruses are united by the homologous replication-associated protein (Rep). An accurate genealogy of Rep can therefore provide insights into how these diverse families are related to each other. We used a dataset of eukaryote-associated CRESS DNA RefSeq genomes (n=926), which included representatives from all six established families and unclassified species. To assure an optimal Rep genealogy, we derived and tested a bespoke amino acid substitution model (named CRESS), which outperformed existing protein matrices in describing the evolution of Rep. The CRESS model-estimated Rep genealogy resolved the monophyly of Bacilladnaviridae and the reciprocal monophyly of Nanoviridae and the alpha-satellites when trees estimated with general matrices like LG did not. The most intriguing, previously unobserved result is a likely single origin of intron-containing Reps, which causes several geminivirus genera to group with Genomoviridae (bootstrap support 55%, aLRT SH-like support 0.997, 0.91-0.997 in trees estimated with established matrices). This grouping, which eliminates the monophyly of Geminiviridae, is supported by both domains of Rep, and appears to be related to our use of all RefSeq Reps instead of subsampling to get a smaller dataset. In addition to producing a trustworthy Rep genealogy, the derived CRESS matrix is proving useful for other analyses; it best fit alignments of capsid protein sequences from several CRESS DNA families and parvovirus NS1/Rep sequences.
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eukaryotic circular rep encoding single stranded dna cress dna Viruses ubiquitous Viruses with small genomes and a diverse host range
Advances in Virus Research, 2019Co-Authors: Lele Zhao, Mya Breitbart, Karyna Rosario, Siobain DuffyAbstract:Abstract While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for Viruses, modern metagenomics sequencing has revealed circular ssDNA Viruses in most environments and in association with diverse hosts. In particular, circular ssDNA Viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA Viruses (CRESS DNA) Viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiViruses and circoViruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA Viruses, and speculates on future research horizons.
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A field guide to eukaryotic circular single-stranded DNA Viruses: insights gained from metagenomics
Archives of Virology, 2012Co-Authors: Karyna Rosario, Siobain Duffy, Mya BreitbartAbstract:Despite their small size and limited protein-coding capacity, the rapid evolution rates of single-stranded DNA (ssDNA) Viruses have led to their emergence as serious plant and animal pathogens. Recently, metagenomics has revealed an unprecedented diversity of ssDNA Viruses, expanding their known environmental distributions and host ranges. This review summarizes and contrasts the basic characteristics of known circular ssDNA viral groups, providing a resource for analyzing the wealth of ssDNA viral sequences identified through metagenomics. Since ssDNA Viruses are largely identified based on conserved rolling circle replication proteins, this review highlights distinguishing motifs and catalytic residues important for replication. Genomes identified through metagenomics have demonstrated unique ssDNA viral genome architectures and revealed characteristics that blur the boundaries between previously well-defined groups. Metagenomic discovery of ssDNA Viruses has created both a challenge to current taxonomic classification schemes and an opportunity to revisit hypotheses regarding the evolutionary history of these Viruses.
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diverse circovirus like genome architectures revealed by environmental metagenomics
Journal of General Virology, 2009Co-Authors: Karyna Rosario, Siobain Duffy, Mya BreitbartAbstract:Single-stranded DNA (ssDNA) Viruses with circular genomes are the smallest Viruses known to infect eukaryotes. The present study identified 10 novel genomes similar to ssDNA circoViruses through data-mining of public viral metagenomes. The metagenomic libraries included samples from reclaimed water and three different marine environments (Chesapeake Bay, British Columbia coastal waters and Sargasso Sea). All the genomes have similarities to the replication (Rep) protein of circoViruses; however, only half have genomic features consistent with known circoViruses. Some of the genomes exhibit a mixture of genomic features associated with different families of ssDNA Viruses (i.e. circoViruses, geminiViruses and parvoViruses). Unique genome architectures and phylogenetic analysis of the Rep protein suggest that these Viruses belong to novel genera and/or families. Investigating the complex community of ssDNA Viruses in the environment can lead to the discovery of divergent species and help elucidate evolutionary links between ssDNA Viruses.
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phylogenetic evidence for rapid rates of molecular evolution in the single stranded dna begomovirus tomato yellow leaf curl virus
Journal of Virology, 2008Co-Authors: Siobain Duffy, Edward C HolmesAbstract:for protein-coding regions. The intergenic region, which is known to be more variable, was found to evolve even more rapidly, with a mean substitution rate of 1.56 10 3 subs/site/year. Notably, these substitution rates, the first reported for a plant DNA virus, are in line with those estimated previously for mammalian ssDNA Viruses and RNA Viruses. Our results therefore suggest that the high evolutionary rate of the geminiViruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts.
Mya Breitbart - One of the best experts on this subject based on the ideXlab platform.
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Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA
'American Society for Microbiology', 2020Co-Authors: Kema Malki, Karyna Rosario, Michael J Tisza, Natalie A. Sawaya, Anna J. Székely, Mya BreitbartAbstract:Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida’s first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida’s first-magnitude springs, providing a baseline against which to compare future ecosystem change.Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 103 ml−1 to 1.1 × 105 ml−1 and 2.2 × 103 ml−1 to 3.4 × 104 ml−1, respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) Viruses. Sequences similar to those of ssDNA Viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small Viruses merit further investigation in groundwater systems
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Distributed under Creative Commons CC-BY 4.0 Towards quantitative viromics for both double-stranded and single-stranded DNA Viruses
2020Co-Authors: Simon Roux, Mya Breitbart, Natalie Solonenko, Vinh T Dang, Bonnie T Poulos, Sarah M Schwenck, Dawn B Goldsmith, Maureen L Coleman, Matthew B. SullivanAbstract:ABSTRACT Background. Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated Viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of nondsDNA Viruses nearly unknown, including single-stranded DNA (ssDNA) Viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods. Here we designed mock viral communities including both ssDNA and dsDNA Viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA Viruses. Results. Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA Viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA Viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryoteinfecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) Viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion. Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems
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Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA
'American Society for Microbiology', 2020Co-Authors: Kema Malki, Karyna Rosario, Michael J Tisza, Natalie A. Sawaya, Anna J. Székely, Mya BreitbartAbstract:ABSTRACT Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 103 ml−1 to 1.1 × 105 ml−1 and 2.2 × 103 ml−1 to 3.4 × 104 ml−1, respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) Viruses. Sequences similar to those of ssDNA Viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small Viruses merit further investigation in groundwater systems. IMPORTANCE Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida’s first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida’s first-magnitude springs, providing a baseline against which to compare future ecosystem change
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eukaryotic circular rep encoding single stranded dna cress dna Viruses ubiquitous Viruses with small genomes and a diverse host range
Advances in Virus Research, 2019Co-Authors: Lele Zhao, Mya Breitbart, Karyna Rosario, Siobain DuffyAbstract:Abstract While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for Viruses, modern metagenomics sequencing has revealed circular ssDNA Viruses in most environments and in association with diverse hosts. In particular, circular ssDNA Viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA Viruses (CRESS DNA) Viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiViruses and circoViruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA Viruses, and speculates on future research horizons.
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novel circular single stranded dna Viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins
Frontiers in Microbiology, 2015Co-Authors: Karyna Rosario, Ryan O Schenck, Rachel C Harbeitner, Stephanie N Lawler, Mya BreitbartAbstract:Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) Viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) Viruses were originally thought to only infect plants and vertebrates, recent studies have identified these Viruses in a number of invertebrates. To further explore CRESS-DNA Viruses in the marine environment, this study surveyed CRESS-DNA Viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported Viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA Viruses that included approximately one third of the marine invertebrate associated Viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA Viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these Viruses.
Karyna Rosario - One of the best experts on this subject based on the ideXlab platform.
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Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA
'American Society for Microbiology', 2020Co-Authors: Kema Malki, Karyna Rosario, Michael J Tisza, Natalie A. Sawaya, Anna J. Székely, Mya BreitbartAbstract:Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida’s first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida’s first-magnitude springs, providing a baseline against which to compare future ecosystem change.Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 103 ml−1 to 1.1 × 105 ml−1 and 2.2 × 103 ml−1 to 3.4 × 104 ml−1, respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) Viruses. Sequences similar to those of ssDNA Viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small Viruses merit further investigation in groundwater systems
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Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA
'American Society for Microbiology', 2020Co-Authors: Kema Malki, Karyna Rosario, Michael J Tisza, Natalie A. Sawaya, Anna J. Székely, Mya BreitbartAbstract:ABSTRACT Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 103 ml−1 to 1.1 × 105 ml−1 and 2.2 × 103 ml−1 to 3.4 × 104 ml−1, respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) Viruses. Sequences similar to those of ssDNA Viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small Viruses merit further investigation in groundwater systems. IMPORTANCE Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida’s first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida’s first-magnitude springs, providing a baseline against which to compare future ecosystem change
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eukaryotic circular rep encoding single stranded dna cress dna Viruses ubiquitous Viruses with small genomes and a diverse host range
Advances in Virus Research, 2019Co-Authors: Lele Zhao, Mya Breitbart, Karyna Rosario, Siobain DuffyAbstract:Abstract While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for Viruses, modern metagenomics sequencing has revealed circular ssDNA Viruses in most environments and in association with diverse hosts. In particular, circular ssDNA Viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA Viruses (CRESS DNA) Viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiViruses and circoViruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA Viruses, and speculates on future research horizons.
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novel circular single stranded dna Viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins
Frontiers in Microbiology, 2015Co-Authors: Karyna Rosario, Ryan O Schenck, Rachel C Harbeitner, Stephanie N Lawler, Mya BreitbartAbstract:Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) Viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) Viruses were originally thought to only infect plants and vertebrates, recent studies have identified these Viruses in a number of invertebrates. To further explore CRESS-DNA Viruses in the marine environment, this study surveyed CRESS-DNA Viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported Viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA Viruses that included approximately one third of the marine invertebrate associated Viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA Viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these Viruses.
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High Global Diversity of CycloViruses Amongst Dragonflies
Journal of General Virology, 2013Co-Authors: Anisha Dayaram, Milen Marinov, Gerardo R. Argüello-astorga, Mya Breitbart, Karyna Rosario, Kristen A. Potter, Angela B. Moline, Dana Drake Rosenstein, John E. Thomas, Arvind VarsaniAbstract:Members of the family Circoviridae, specifically the genus Circovirus, were thought to infect only vertebrates; however, members of a sister group under the same family, the proposed genusCyclovirus, have been detected recently in insects. In an effort to explore the diversity of cycloViruses and better understand the evolution of these novel ssDNA Viruses, here we present five cycloViruses isolated from three dragonfly species (Orthetrum sabina, Xanthocnemis zealandica and Rhionaeschna multicolor) collected in Australia, New Zealand and the USA, respectively. The genomes of these five Viruses share similar genome structure to other cycloViruses, with a circular ~1.7 kb genome and two major bidirectionally transcribed ORFs. The genomic sequence data gathered during this study were combined with all cyclovirus genomes available in public databases to identify conserved motifs and regulatory elements in the intergenic regions, as well as determine diversity and recombinant regions within their genomes. The genomes reported here represent four different cyclovirus species, three of which are novel. Our results confirm that cycloViruses circulate widely in winged-insect populations; in eight different cyclovirus species identified in dragonflies to date, some of these exhibit a broad geographical distribution. Recombination analysis revealed both intra-and inter-species recombination events amongst cycloViruses, including genomes recovered from disparate sources (e.g. goat meat and human faeces). Similar to other well-characterized circular ssDNA Viruses, recombination may play an important role in cyclovirus evolution. © 2013 SGM.
