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Published on: July 27, 2018
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DNA-dependent RNA polymerase detects hidden giant viruses in published databanks
Vikas Sharma1, Philippe Colson2, Roch Giorgi3
1Aix-Marseille Univ., Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Marseille, FranceAix-Marseille Univ., I2M UMR-CNRS 7373, Evolution Biologique et Modélisation, Marseille, France.
Genome Biology and Evolution
|June 15, 2014
Summary
Scientists discovered a new way to identify unknown viruses in environmental DNA. By analyzing DNA-dependent RNA polymerase (RNAP) genes, they can explore the "viral dark matter" missed by traditional methods.
Area of Science:
- Microbiology
- Virology
- Bioinformatics
Background:
- Environmental metagenomics often identifies a significant portion of DNA sequences as
- Ribosomal DNA (rDNA) sequencing misses giant viruses, limiting our understanding of microbial diversity.
Purpose of the Study:
- To investigate the potential of DNA-dependent RNA polymerase (RNAP) genes for identifying previously unknown microbial and viral sequences.
- To explore the
Main Methods:
- Phylogenetic reconstruction of DNA-dependent RNA polymerase subunit 2 (RNAP2) sequences.
- Analysis of viral RNAP2 and reconstruction of putative ancestral RNAP2.
- Comparison of RNAP2-based detection with existing sequence identification methods.
Main Results:
- Identified an overlooked giant virus within the genome of Hydra magnipapillata.
- RNAP2-based methods significantly improved the detection of distant viral clades compared to current sequences.
- Discovered two novel mimiviruses misclassified in existing databases and identified additional putative viral clades.
Conclusions:
- DNA-dependent RNA polymerase (RNAP) genes are a superior marker for exploring environmental DNA dark matter and identifying giant viruses.
- Systematic use of RNAP analysis can enhance the discovery of novel viral diversity in metagenomic studies.
Keywords:
DNA-dependent RNA polymeraseMimivirusdark matterdomains of lifeenvironmentgiant virusmetagenomes“Megavirales”More Related Videos
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