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Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae

Description

With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus

With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2–2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display ∼47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we establish a 78% genome-wide pairwise identity as a species demarcation threshold. Furthermore, using a Rep sequence phylogeny-based analysis coupled with the current knowledge on the classification of geminiviruses, we establish nine genera within the Genomoviridae family. These are Gemycircularvirus (n = 73), Gemyduguivirus (n = 1), Gemygorvirus (n = 9), Gemykibivirus (n = 29), Gemykolovirus (n = 3), Gemykrogvirus (n = 3), Gemykroznavirus (n = 1), Gemytondvirus (n = 1), Gemyvongvirus (n = 1). The presented taxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an example for future classification of other groups of uncultured viruses discovered using metagenomics approaches.

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Created

Date Created
  • 2017-02-02

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Genomovirus Genomes Recovered from Echinothrips americanus Sampled in Florida, USA

Description

Four genomovirus genomes were recovered from thrips (Echinothrips americanus) collected in Florida, USA. These represent four new species which are members of the Gemycircularvirus (n = 2), Gemyduguivirus (n =

Four genomovirus genomes were recovered from thrips (Echinothrips americanus) collected in Florida, USA. These represent four new species which are members of the Gemycircularvirus (n = 2), Gemyduguivirus (n = 1), and Gemykibivirus (n = 1) genera. This is the first record, to our knowledge, of genomoviruses associated with a phytophagous insect.

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Created

Date Created
  • 2017-05-25

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Complete Genome Sequence of a Genomovirus Associated with Common Bean Plant Leaves in Brazil

Description

A new genomovirus has been identified in three common bean plants in Brazil. This virus has a circular genome of 2,220 nucleotides and 3 major open reading frames. It shares

A new genomovirus has been identified in three common bean plants in Brazil. This virus has a circular genome of 2,220 nucleotides and 3 major open reading frames. It shares 80.7% genome-wide pairwise identity with a genomovirus recovered from Tongan fruit bat guano.

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Created

Date Created
  • 2016-11-10

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Novel Single-Stranded DNA Virus Genomes Recovered from Chimpanzee Feces Sampled from the Mambilla Plateau in Nigeria

Description

Metagenomic approaches are rapidly expanding our knowledge of the diversity of viruses. In the fecal matter of Nigerian chimpanzees we recovered three gokushovirus genomes, one circular replication-associated protein encoding single-stranded DNA virus (CRESS), and a CRESS DNA molecule.

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Created

Date Created
  • 2017-03-02

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Genome Sequences of Beet curly top Iran virus, Oat dwarf virus, Turnip curly top virus, and Wheat dwarf virus Identified in Leafhoppers

Description

Implementation of a vector-enabled metagenomics approach resulted in the identification of various geminiviruses. We identified the genome sequences of Beet curly top Iran virus, Turnip curly top viruses, Oat dwarf

Implementation of a vector-enabled metagenomics approach resulted in the identification of various geminiviruses. We identified the genome sequences of Beet curly top Iran virus, Turnip curly top viruses, Oat dwarf viruses, the first from Iran, and Wheat dwarf virus from leafhoppers feeding on beet, parsley, pumpkin, and turnip plants.

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Created

Date Created
  • 2017-02-23

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Genome Sequence of Cauliflower Mosaic Virus Identified in Earwigs (Doru luteipes) through a Metagenomic Approach

Description

Here we report the first complete genome sequence of a cauliflower mosaic virus from Brazil, obtained from the gut content of the predator earwig (Doru luteipes). This virus has a

Here we report the first complete genome sequence of a cauliflower mosaic virus from Brazil, obtained from the gut content of the predator earwig (Doru luteipes). This virus has a genome of 8,030 nucleotides (nt) and shares 97% genome-wide identity with an isolate from Argentina.

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Created

Date Created
  • 2017-03-16

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Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion

Description

Background
In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane

Background
In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses.
Methods
A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3.
Results
We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion.
Conclusions
As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.

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Created

Date Created
  • 2017-07-28

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Genome Sequence of a Podovirus (AAPEc6) Isolated from Wastewater in New Zealand That Infects Escherichia coli O45: H10

Description

Bacteriophages are ideal candidates for pathogen biocontrol to mitigate outbreaks of prevalent foodborne pathogens, such as Escherichia coli. We identified a bacteriophage (AAPEc6) from wastewater that infects E. coli O45:H10.

Bacteriophages are ideal candidates for pathogen biocontrol to mitigate outbreaks of prevalent foodborne pathogens, such as Escherichia coli. We identified a bacteriophage (AAPEc6) from wastewater that infects E. coli O45:H10. The AAPEc6 genome sequence shares 93% identity (with 92% coverage) to enterobacterial phage K1E (Sp6likevirus) in the Autographivirinae subfamily (Podoviridae).

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Created

Date Created
  • 2017-08-03