Welcome to CRESSdna.org




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Maximum likelihood tree built using CRESS matrix. Light green for Geminiviridae, pink for Genomoviridae, blue for Smacoviridae, brown for Bacilladnaviridae, dark green for Circoviridae, yellow for Nanoviridae, gold for alphasatellites (Alphasatellitidae)

Part of the National Science Foundation's Assembling the Tree of Life.

Sponsored with a Grant from the National Science Foundation

Bacilladnaviridae

Bacilladnaviridae is a recently proposed family of CRESS viruses that infect diatoms. This family was formerly the unassigned genus Bacilladnavirus which contained a single member, Chaetoceros salsugineum DNA virus 01. In 2017, the availability of whole genome sequences of other potential members of this genus led to the proposal of a new bacilladnavirus classification system. Bacilladnaviridae contains three genera. The former genus Bacilladnavirus was renamed Protobacilladnavirus, and was joined by Diatodnavirus (containing Chaetoceros diatodnavirus 1)and Kieseladnavirus (containing Avon-Heathcote Estuary associated kieseladnavirus 1).

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Chaetoceros spp. 400X
CC-BY Gtm Neer 2015
For more information about Bacilladnaviridae:
ExPASy ViralZone summary of Bacilladnavirus (now Protobacilladnavirus)

Circoviridae

Many animal-infecting CRESS-DNA viruses are classified into the Circoviridae family. There are two genera within the group, the older Circovirus and the more recently codified Cyclovirus, but both are well represented. At least one disease of economic importance is associated with circovirus infections: post-weaning maturation wasting syndrome in pigs (caused in part by porcine circovirus 2, which is now largely controlled through vaccination in commercial hog production). However, several worldwide veterinary diseases are due to circoviruses, including beak and feather disease and fatal acute diarrhea in dogs.

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Gastrointestinal system of dogs infected with dog circovirus (DogCV) with hemorrhaging in stomach and intestines. CC-BY Li et al. 2013
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Immune electron microscopy image of PCV2 (porcine circovirus 2) particles. CC-BY Guo et al. 2011

While some of the environmental isolates assigned to Circoviridae have genomes over 3,000 and 4,000 bases, it also contains some of the smallest genomes of CRESS-DNA viruses – some well-studied circoviruses have genomes ~1700nt long, and circularized putative genomes from metagenomics studies can be even smaller. Most analyzed sequences have two ORFs: the replication-associated protein (Rep, also referred to as the replication initiator protein) and capsid protein (Cp or Cap), with some isolates having had a third ORF experimentally verified, and some sequences having many hypothetical ORFs called that have not yet been studied in the lab.

Both cycloviruses and circoviruses have non-enveloped, icosahedral virions of 15-25nm encapsidating their circular, ssDNA genomes, but while members of Circovirus are found infecting or associated with mammals, birds and fish, cycloviruses have been found infecting or associated with mammals, birds and insects. Sequences assigned to Circovirus have ambisense genomes, with the Rep gene in sense, sequences in Cyclovirus typically are ambisense in the opposite orientation (Rep gene in anti-sense). A great primer on Circoviridae

For more information about Circovirus:
ICTV report on circovirus
ExPASy ViralZone summary of circovirus
Type species: Porcine circovirus 1 (NC_001792.2)

For more information about Cyclovirus:
ICTV report on cyclovirus
ExPASy ViralZone summary of cyclovirus
Type species: Human-associated cyclovirus 8 (KF031466)

Geminiviridae

The family Geminiviridae is the most speciose family in all of virology. It includes nine genera: Becurtovirus, Begomovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastrevirus, Topocuvirus and Turncurtovirus. Members of these genera include devastating plant pathogens that have serious economic consequences. For example, African Cassava Mosaic Virus is one of the viruses causing Cassava Mosaic Disease (CMD). This is particularly an issue in sub-Saharan Africa where the disease severely limits the production of cassava, which is the primary starch source in the region. CMD results in an annual loss of 1.2 to 2.3 billion US dollars in sub-Saharan Africa.
Geminiviruses are non-enveloped ssDNA viruses that have monopartite or bipartite circular genomes that are 2.6 to 5.2 kb long. These viruses are transmitted by insect vectors including whiteflies, leafhoppers, aphids and treehoppers. The host ranges of geminiviruses are vast and include both monocot and dicot plants, both cultivated and uncultivated plants. Geminivirus virions are composed of two incomplete icosahedra in a structure that has been described as twinned or geminate. These virions are around 22 by 38 nm in size and contain only one structural protein (CP).

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African cassava mosaic virus in Eastern Democratic Republic of the Congo.
CC-BY Caroline Gluck/Oxfam International 2012
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Maize streak virus. CC-BY Ed Rybicki

For more information about Geminivirus genera:
Genus ICTV report ExPASy ViralZone summary Type species
Becurtovirus report summary NC_010417
Begomovirus report summary NC_001439
Capulavirus report summary NC_030238
Curtovirus report summary NC_001412
Eragrovirus report summary NC_012664
Grablovirus report summary NC_022002
Mastrevirus report summary NC_001346
Topocuvirus report summary NC_003825
Turncurtovirus report summary NC_014324


Genomoviridae

Until recently, the family Genomoviridae included one genus with a single species, Sclerotinia gemycircularvirus 1 (SsHADV-1) in the genus Gemycircularvirus. Virions of SsHADV-1 are non-enveloped, isometrically shaped, 20-22 nm in diameter and contain one CP (capsid protein) gene. SsHADV-1 has a circular, ssDNA genome of length 2,166 nucleotides encoding two genes, CP and Rep. This virus infects a plant pathogenic fungus and is transmitted by a mycophagous insect, Lycoriella ingenua. In the year 2017, Rep-based phylogenetic analyses of 121 SsHADV-1 like viruses revealed eight additional genera including Gemykibivirus, Gemygorvirus, Gemykolovirus, Gemykrogvirus, Gemyvongvirus, Gemytondvirus, Gemykroznavirus and Gemyduguivirus.

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Sclerotinia sclerotiorum sclerotia on Phaseolus vulgaris bushbean.
CC-BY Rasbak 2009

For more information about Genomoviridae:
ExPASy ViralZone summary of genomoviruses
Type Species (1 of 8): Sclerotinia sclerotiorum hypovirulance associated DNA virus 1 (NC_013116)

Nanoviridae

The plant infecting CRESS-DNA viruses with more than two genomic segments belong in the family Nanoviridae, which includes the genera Babuvirus and Nanovirus. One of the most economically important species in the family Nanoviridae is Banana bunchy top virus (BBTV), the type species of babuvirus. BBTV causes banana bunchy top disease, which is common in banana growing areas such as Southeast Asia, the South Pacific, India and Africa. This virus is transmitted by the banana aphid and causes plant crumpling, shrinking and chlorosis, which may develop into necrosis.

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Banana bunchy top, caused by Banana bunchy top virus (BBTV). CC-BY Scott Nelson 2014.
Viruses in the family Nanoviridae have multipartite genomes consisting of 6 to 8 ~1000 nucleotide segments of circular ssDNA. Five of these DNA components are shared between babuviruses and nanoviruses. (DNA-R, -N, -S, -C and –M). Nanoviruses infect dicots, have 8 genomic DNAs and may include three other DNA components with functions that have yet to be determined (DNA-U1, -U2 and –U4). Babuviruses infect monocots, have 6 genomic DNAs and may include another DNA component with an unknown function (DNA-U4). Each of these components encode a single ORF that is transcribed in one direction, though a second putative ORF has been identified on one segment of BBTV (DNA-R). The virions of these viruses are non-enveloped, sized 17-20nm in diameter and have one CP (coat protein). Additional DNA segments (alphasatellites) are also associated with many viruses in the family and can alter disease symptoms.

For more information about Nanovirus:
ICTV report on nanovirus.
ExPASy ViralZone summary of nanovirus
Type Species: Subterranean clover stunt virus (NC_003818.1)

For more information about Babuvirus:
ICTV report on babuvirus.
ExPASy ViralZone summary of babuvirus
Type Species: Banana bunchy top virus (NC_003479.1)

Smacoviridae

Smacoviridae is a monophyletic group of CRESS DNA viruses that was proposed in 2015. Many of the viruses now classified in this clade were initially named "stool-associated circular virus (SCV)." These viruses were reported in stool samples of cows, chimpanzees, pigs, turkeys and rats. Related viruses have been found in the feces of humans and other primates, including gorillas, lemurs and black howler monkeys. In 2016, viruses like smacoviruses (SmaCV2 and SmaCV3) were detected in stool samples of individuals suffering from diarrhea in Peru. The role of these viruses in the development of diarrhea in infected individuals is unknown but their presence in individuals suffering from diarrhea is intriguing. Additionally, recent fecal analyses have shown that African non-human primates are carriers of smacoviruses.

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Genomic analysis of pig stool-associated ssDNA virus (PigSCV) found in fecal samples of pigs.
CC-BY Sachsenröder et al 2012
Type species (1 of 17): Human smacovirus 1 isolate France/12/2008/3454 (NC_026252)

Classifier



This function is under revision, please check back later.


Resources

ProtTest3 with CRESS DNA virus model

This version of ProtTest was modified from source code "prottest3-3.4.2-release.zip" to include an option for CRESS amino acid substitution matrix. The CRESS amino acid substitution matrix is an specific matrix derived from CRESS DNA viral protein sequences. The CRESS matrix .txt file can also be found inside "models" folder within this compressed file.The details concerning this matrix will be made available through future publication.

Contributors

Professor Mya Breitbart

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Mya Breitbart is a Professor at the University of South Florida in the College of Marine Science. She earned her BS in Biology from Florida Institute of Technology in 2000, and her PhD in Cellular and Molecular Biology from San Diego State University and the University of California, San Diego in 2006. Her research uses metagenomic sequencing to explore the identity, diversity, and distribution of viruses in a wide range of environments, ranging from seawater to sewage. In addition, her laboratory is using viral metagenomics to discover novel viral pathogens causing disease in plants and animals, as well as to explore the environmental reservoirs and transmission mechanisms of these viruses. One common theme among these viral discovery projects has been the identification of eukaryotic circular Rep-encoding ssDNA (CRESS DNA) viruses in a variety of environments and sample types. The ecology of these CRESS DNA viruses is completely unknown, prompting investigation of their diversity, distribution, and host range.
Publications Lab website

Dr. Karyna Rosario

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Lecture given to 7th graders in Puerto Rico during a two-day outreach activity called What's bugging My Bug?! in 2014. During the outreach, students learned about viruses while helping to collect insects for CRESS DNA virus discovery.
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Dr. Karyna Rosario is a research associate at the Marine Genomics Laboratory led by Dr. Mya Breitbart at the University of South Florida (USF). She completed her Ph.D. in Biological Oceanography with an emphasis on environmental virology at USF. Throughout her career, Dr. Rosario has employed metagenomic approaches to describe viral diversity in different environments and organisms. Since her research has uncovered a diversity of circular Rep-encoding single-stranded (CRESS) DNA viruses in unexpected organisms, recent work focuses on investigating novel CRESS DNA viruses in undersampled invertebrate taxa and their evolutionary relationships to vertebrate- and plant-infecting ssDNA viruses.
Publications Lab website

Hector G. Loyola Irizarry

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Hector G. Loyola Irizarry of the University of Puerto Rico Mayagüez presenting his work on codon usage bias and strandedness in CRESS DNA viral genomes at the RiSE at Rutgers 2017 poster symposium. This work was conducted at the Duffy lab at Rutgers University in New Brunswick, NJ.

Professor Siobain Duffy

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Siobain is an Associate Professor in the Department of Ecology, Evolution and Natural Resources. She is interested in the molecular evolution of fast-evolving viruses, specifically those with RNA and single-stranded DNA genomes She studies the emergence of viruses on novel hosts using experimental evolution, conducts computational research on emergent RNA and ssDNA viruses, and improves phylogenetic methods for viral molecular epidemiology.
Publications Lab website

Dr. Erik Lavington

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Erik is interested in group-level genetics and computational methods. He received his his B.S in Biology at the University of Kansas and his PhD in Genetics at Stony Brook University. His PhD thesis combined population and experimental genetics in fruit flies to generate hypotheses of metabolic flux control in the glycolysis/gluconeogenesis pathway. He continued his work in population genetics of fruit flies in Andrew Kern's lab, studying the effects of large chromosomal inversions on genome-wide patterns of gene expression. He is currently contributing to knowledge and methods for circular rep-encoding single-stranded DNA (CRESS DNA) virus phylogeny by using machine learning methods for classification and feature selection in CRESS DNA viruses.
Publications

Dr. Lele Zhao

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Lele has a Bachelor of Science in Biotechnology from Beijing Normal University and a PhD (advisor: Dr. Siobain Duffy) in Microbial Biology from Rutgers University. She is currently a postdoctoral researcher in the Pathogen Dynamics group led by Prof Christophe Fraser at the Big Data Institute at the University of Oxford. Lele is generally interested in evolution of fast-evolving viruses and applying various methods (computational and experimental) to study within-host and between-host viral evolution. She has worked with dsRNA bacteriophage phi6 and eukaryote-infecting circular Rep-encoding ssDNA (CRESS DNA) viruses and is currently working on HIV.

Contact

Please refer inquiries to Siobain Duffy

Email: duffy [at] sebs [dot] rutgers [dot] edu

Phone: 848 932 6299

Mail:
Rutgers University
Foran Hall Room 316
59 Dudley Road
New Brunswick, 08901

Results

Results from Taxonomy prediction