MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

Noguchi, Hideki; Taniguchi, Tadatsugu; Itoh, Takehiko

doi:10.1093/dnares/dsn027

Cited by 581 publications

(460 citation statements)

References 35 publications

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“…A BLASTx search was computed to detect contigs containing genes similar to those of RNA viruses (extracted from the NCBI protein database on Aug 2012). Genes were predicted with MetaGeneAnnotator 60 for all contigs that were found to encode putative RNA virus capsidlike proteins (threshold of 50 on bitscore and 0.001 on e-value). Contigs containing at least two genes, one similar to an RNA virus capsid gene and one to the RC-Rep gene were considered as CHIVs (Supplementary Data 1).…”

Section: Methodsmentioning

confidence: 99%

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

et al. 2013

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Metagenomic studies have uncovered an astonishing diversity of ssDNA viruses encoding replication proteins (Reps) related to those of eukaryotic Circoviridae, Geminiviridae or Nanoviridae; however, exact evolutionary relationships among these viruses remain obscure. Recently, a unique chimeric virus (CHIV) genome, which has apparently emerged via recombination between ssRNA and ssDNA viruses, has been discovered. Here we report on the assembly of 13 new CHIV genomes recovered from various environments. Our results indicate a single event of capsid protein (CP) gene capture from an RNA virus in the history of this virus group. The domestication of the CP gene was followed by an unprecedented recurrent replacement of the Rep genes in CHIVs with distant counterparts from diverse ssDNA viruses. We suggest that parasitic and symbiotic interactions between unicellular eukaryotes were central for the emergence of CHIVs and that such turbulent evolution was primarily dictated by incongruence between the CP and Rep proteins.

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Section: Methodsmentioning

confidence: 99%

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

et al. 2013

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“…ORFs were predicted for sequence reads in each virome using MetageneAnnotator (52) and translated. Translated ORFs were queried against a reference protein database of RNR representative sequences from UniRef90 RNR clusters (53) using BLASTp (54) with an e-value cutoff of 1e-10.…”

Section: Methodsmentioning

confidence: 99%

Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses

Sakowski¹,

Munsell²,

Hyatt³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Virioplankton play a crucial role in aquatic ecosystems as topdown regulators of bacterial populations and agents of horizontal gene transfer and nutrient cycling. However, the biology and ecology of virioplankton populations in the environment remain poorly understood. Ribonucleotide reductases (RNRs) are ancient enzymes that reduce ribonucleotides to deoxyribonucleotides and thus prime DNA synthesis. Composed of three classes according to O 2 reactivity, RNRs can be predictive of the physiological conditions surrounding DNA synthesis. RNRs are universal among cellular life, common within viral genomes and virioplankton shotgun metagenomes (viromes), and estimated to occur within >90% of the dsDNA virioplankton sampled in this study. RNRs occur across diverse viral groups, including all three morphological families of tailed phages, making these genes attractive for studies of viral diversity. Differing patterns in virioplankton diversity were clear from RNRs sampled across a broad oceanic transect. The most abundant RNRs belonged to novel lineages of podoviruses infecting α-proteobacteria, a bacterial class critical to oceanic carbon cycling. RNR class was predictive of phage morphology among cyanophages and RNR distribution frequencies among cyanophages were largely consistent with the predictions of the "kill the winner-cost of resistance" model. RNRs were also identified for the first time to our knowledge within ssDNA viromes. These data indicate that RNR polymorphism provides a means of connecting the biological and ecological features of virioplankton populations. viral ecology | viral evolution | phage replication

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“…Open reading frames (ORFs) were predicted from all virome reads using MetageneAnnotator (Noguchi et al, 2006(Noguchi et al, , 2008, translated and subsequently clustered (supplementary methods) at a similarity cutoff of 40% (Edgar, 2010). Representative sequences from all of the peptide clusters were searched in the VIROME database to determine which clusters contained a representative peptide sequence with significant homology (BLASTP E-score p10 À 3 ) to a known DNA polymerase.…”

Section: Metagenomic and Phylogenetic Analysismentioning

confidence: 99%

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

et al. 2013

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Virioplankton have a significant role in marine ecosystems, yet we know little of the predominant biological characteristics of aquatic viruses that influence the flow of nutrients and energy through microbial communities. Family A DNA polymerases, critical to DNA replication and repair in prokaryotes, are found in many tailed bacteriophages. The essential role of DNA polymerase in viral replication makes it a useful target for connecting viral diversity with an important biological feature of viruses. Capturing the full diversity of this polymorphic gene by targeted approaches has been difficult; thus, full-length DNA polymerase genes were assembled out of virioplankton shotgun metagenomic sequence libraries (viromes). Within the viromes novel DNA polymerases were common and found in both double-stranded (ds) DNA and single-stranded (ss) DNA libraries. Finding DNA polymerase genes in ssDNA viral libraries was unexpected, as no such genes have been previously reported from ssDNA phage. Surprisingly, the most common virioplankton DNA polymerases were related to a siphovirus infecting an a-proteobacterial symbiont of a marine sponge and not the podoviral T7-like polymerases seen in many other studies. Amino acids predictive of catalytic efficiency and fidelity linked perfectly to the environmental clades, indicating that most DNA polymerase-carrying virioplankton utilize a lower efficiency, higher fidelity enzyme. Comparisons with previously reported, PCR-amplified DNA polymerase sequences indicated that the most common virioplankton metagenomic DNA polymerases formed a new group that included siphoviruses. These data indicate that slower-replicating, lytic or lysogenic phage populations rather than fast-replicating, highly lytic phages may predominate within the virioplankton.

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MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

Cited by 581 publications

References 35 publications

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

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